{"entity": "publications", "timestamp": "2026-06-15T20:23:56.774Z", "year": "2026", "links": {"self": {"href": "https://publications.scilifelab.se/publications/2026.json"}, "display": {"href": "https://publications.scilifelab.se/publications/2026"}}, "publications_count": 141, "full": true, "publications": [{"entity": "publication", "iuid": "2d4022b436484360aa5abc58c422de2b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d4022b436484360aa5abc58c422de2b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d4022b436484360aa5abc58c422de2b"}}, "title": "When the proteome meets the metabolome observational and Mendelian randomization analyses.", "authors": [{"family": "Zheng", "given": "Rui", "initials": "R"}, {"family": "Delgado-Velandia", "given": "Mario", "initials": "M"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Dekkers", "given": "Koen F", "initials": "KF"}, {"family": "Lundmark", "given": "Per", "initials": "P"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Lind", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2026-07-00", "journal": {"title": "Metabolism", "issn": "1532-8600", "volume": "180", "pages": "156602", "issn-l": "0026-0495"}, "abstract": "The basis for protein synthesis is the genetic code. Many of these proteins will affect intermediary metabolites by acting as enzymes, hormones, or by other actions. The aim of the present study was to assess the relationships of a large number of proteins with endogenous metabolites.\n\nPlasma protein levels were measured by the proximity extension assay (PEA) and metabolites by mass spectrometry. Cross-sectional relationships of 242 proteins and 790 metabolites were evaluated in the EpiHealth and POEM studies using a discovery/validation approach. Genetic instruments identified in UK Biobank for protein levels (n = 1621) and genetics for metabolite levels (n = 777) in SCAPIS and EpiHealth were employed for Mendelian randomization (MR) analysis regarding putative causal associations.\n\nIn the observational analyses, 20% of the evaluated pairwise protein-metabolite associations were found significant in both the discovery and validation samples. We could however only find support for causal effects in the MR analysis for <0.1% of the pairwise associations, representing 326 unique proteins. The R2 for the relationship between the MR and observational estimates was only 0.05. 37 protein-metabolite relationships that were significant in a congruent fashion in both the observational and MR analyses were identified. A searchable online protein vs metabolite atlas was created for the scientific community to use these results. We also give some examples where metabolites were used to enhance protein findings in cardiovascular epidemiological research.\n\nThis study provides a comprehensive assessment of a large number of protein- metabolite relationships using both observational and MR analyses, highlighting how these results could be used to enhance clinical research.", "doi": "10.1016/j.metabol.2026.156602", "pmid": "41962653", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0026-0495(26)00112-5"}], "notes": [], "created": "2026-06-01T08:45:40.108Z", "modified": "2026-06-01T08:45:40.112Z"}, {"entity": "publication", "iuid": "7561bb26ddda43b5a3408ef3a974ac88", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7561bb26ddda43b5a3408ef3a974ac88.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7561bb26ddda43b5a3408ef3a974ac88"}}, "title": "Paleogenomes reveal the evolutionary relationship between modern and cave lions.", "authors": [{"family": "Stanton", "given": "David W G", "initials": "DWG"}, {"family": "Bergstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Carmagnini", "given": "Alberto", "initials": "A"}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Pawar", "given": "Harvinder", "initials": "H"}, {"family": "Sandoval-Velasco", "given": "Marcela", "initials": "M"}, {"family": "Androsov", "given": "Semyon", "initials": "S"}, {"family": "Fedorov", "given": "Sergey", "initials": "S"}, {"family": "Kuhlwilm", "given": "Martin", "initials": "M"}, {"family": "Nagel", "given": "Doris", "initials": "D"}, {"family": "Plotnikov", "given": "Valeri", "initials": "V"}, {"family": "Protopopov", "given": "Albert", "initials": "A"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Barnett", "given": "Ross", "initials": "R"}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T"}, {"family": "Yamaguchi", "given": "Nobuyuki", "initials": "N"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Frantz", "given": "Laurent", "initials": "L"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2026-06-03", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674"}, "abstract": "The Eurasian cave lion was abundant across the Northern Hemisphere before the Late Pleistocene megafaunal extinctions. However, the extent of the distinction between cave and modern lions and their adaptive differences have remained unclear. Using 12 cave lion genomes spanning more than 100,000 years, we show that modern and cave lions were distinct evolutionary lineages with separate demographic histories and unique non-synonymous variants. We also identify evidence of ancient gene flow between them, with the best modern lion proxy for this ancestry being an extinct Southwest Asian population. This admixture correlates with global ice extent, with 3.2%-4.4% modern lion ancestry detected in a \u223c20,000-year-old cave lion from Central East Asia. These findings provide insight into the evolutionary history of the cave lion, once one of the Northern Hemisphere's most ecologically impactful megafaunal species.", "doi": "10.1016/j.cell.2026.05.007", "pmid": "42235515", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(26)00524-6"}], "notes": [], "created": "2026-06-08T18:01:11.696Z", "modified": "2026-06-08T18:01:11.713Z"}, {"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", "volume": "8", "issue": "2", "pages": "lqag053", "issn-l": null}, "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"}, "xrefs": [{"db": "pmc", "key": "PMC13202175"}, {"db": "pii", "key": "lqag053"}], "notes": [], "created": "2026-06-08T17:20:13.126Z", "modified": "2026-06-08T17:20:13.152Z"}, {"entity": "publication", "iuid": "9bafa70241894ebcab4e2bf9d0640d40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9bafa70241894ebcab4e2bf9d0640d40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9bafa70241894ebcab4e2bf9d0640d40"}}, "title": "Comparing DNA metabarcoding with light microscopy to identify eukaryotic phytoplankton in the Baltic Sea, Kattegat and Skagerrak.", "authors": [{"family": "Torstensson", "given": "Anders", "initials": "A"}, {"family": "Brugel", "given": "Sonia", "initials": "S"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Hedblom", "given": "Mikael", "initials": "M"}, {"family": "Jurdzinski", "given": "Krzysztof T", "initials": "KT"}, {"family": "Karlson", "given": "Bengt", "initials": "B"}, {"family": "Latz", "given": "Meike A C", "initials": "MAC"}, {"family": "Lindh", "given": "Markus", "initials": "M"}, {"family": "Lycken", "given": "Jenny", "initials": "J"}, {"family": "Andersson", "given": "Agneta", "initials": "A"}], "type": "journal article", "published": "2026-05-19", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "Marine phytoplankton monitoring has long relied on microscopy, but DNA metabarcoding has recently emerged as a complementary approach. This study assessed the applicability of DNA metabarcoding of the 18S ribosomal RNA gene in marine monitoring and compared its results with conventional microscopy. We analyzed data from 232 surface water samples from 17 monitoring stations in the Baltic Sea, Kattegat, and Skagerrak. Metabarcoding detected more orders, genera, and species than microscopy, with a 43% overlap in the most common genera identified by both methods. Despite attempts to normalize sequence reads to spike-in DNA or DNA concentrations, the correlations between abundances derived from the two methods were weak, though varied considerably between taxonomic groups and geographical areas. Correlations were consistently stronger when using carbon and biovolume concentrations than cell abundances. Our results highlight the potential of metabarcoding to expand biodiversity assessments and advance our understanding of microbial biodiversity in marine ecosystems. As a complement to microscopy, it can enhance existing monitoring efforts. Future improvements in reference database completeness, adoption of long-read sequencing technologies, and better characterization of gene copy number variability per cell are needed to further extend the applicability of metabarcoding for quantitative analyses.", "doi": "10.1038/s41598-026-48838-z", "pmid": "42156811", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13190673"}, {"db": "pii", "key": "10.1038/s41598-026-48838-z"}], "notes": [], "created": "2026-06-08T17:17:40.513Z", "modified": "2026-06-08T17:17:40.517Z"}, {"entity": "publication", "iuid": "69e64360fa0d42d4a7da65ad33e6a6c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69e64360fa0d42d4a7da65ad33e6a6c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69e64360fa0d42d4a7da65ad33e6a6c4"}}, "title": "Systematic discovery of motif-based interactions of the auxiliary domains of USP family deubiquitinases.", "authors": [{"family": "Konstantinou", "given": "Aimiliani", "initials": "A", "orcid": "0009-0009-6955-9906", "researcher": {"href": "https://publications.scilifelab.se/researcher/adbee78c31e648518a914fd366c29be5.json"}}, {"family": "C\u00f3rdova-P\u00e9rez", "given": "Alicia", "initials": "A"}, {"family": "Varga", "given": "Julia K", "initials": "JK", "orcid": "0000-0002-5318-2798", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cce1545060342798144f3c8144d4d64.json"}}, {"family": "Madhu", "given": "Priyanka", "initials": "P"}, {"family": "Simonetti", "given": "Leandro", "initials": "L", "orcid": "0000-0003-1283-9770", "researcher": {"href": "https://publications.scilifelab.se/researcher/23530c1a3cef4f499a460ac59c674261.json"}}, {"family": "Vieler", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-3617-1018", "researcher": {"href": "https://publications.scilifelab.se/researcher/d02f57d8ee554f1895fb5cf5d93541ef.json"}}, {"family": "Ishimura", "given": "Ryosuke", "initials": "R"}, {"family": "Lamoliatte", "given": "Frederic", "initials": "F"}, {"family": "Schueler-Furman", "given": "Ora", "initials": "O", "orcid": "0000-0002-1624-0362", "researcher": {"href": "https://publications.scilifelab.se/researcher/5332c64faf114b16bf4a5b5e789d5aa3.json"}}, {"family": "Davey", "given": "Norman E", "initials": "NE", "orcid": "0000-0001-6988-4850", "researcher": {"href": "https://publications.scilifelab.se/researcher/c239a7f1b8a344948d80b9104a5fcc96.json"}}, {"family": "Kulathu", "given": "Yogesh", "initials": "Y", "orcid": "0000-0002-3274-1642", "researcher": {"href": "https://publications.scilifelab.se/researcher/1646c4f2949a4a7ea47be413a9a770db.json"}}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}], "type": "journal article", "published": "2026-05-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723"}, "abstract": "The ubiquitin-specific proteases (USPs) family is the largest family of human deubiquitinating enzymes (DUBs). While most USPs are agnostic to polyubiquitin linkage-type, their substrate specificity is thought to be mediated by the recognition of the ubiquitnated protein itself. In addition to their catalytic domain, USPs have one or more auxiliary domains (ADs) with key functions in regulating DUB activity and localization. We hypothesize that some ADs bind short linear motifs (SLiMs) typically found in intrinsically disordered regions of proteins to achieve targeting to substrates and multiprotein complexes. To test this, we systematically assess the potential of 29 USP-ADs and two full-length USPs for SLiM binding using a combination of proteomic-peptide phage display, peptide SPOT arrays and affinity measurements. We discover SLiM-based interactions for 14 ADs from 9 USP-DUBs, including CYLD, USP11, USP19, USP20, USP22 and USP33, and define the consensus motif and properties of the SLiM-AD binding. Interestingly, we establish that the zf-UBP and DUSP2 domains of USP20 and USP33 are SLiM binding ADs with similar binding profiles, explaining the functional redundancy between the two DUBs. Our work reveals unique motifs recognized by the auxiliary domains CAP-Gly, UBL, zf-UBP and DUSP, with potential functional implications for substrate recognition and complex assemblies.", "doi": "10.1038/s41467-026-73047-7", "pmid": "42151178", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-026-73047-7"}], "notes": [], "created": "2026-06-08T17:42:03.867Z", "modified": "2026-06-08T17:42:04.152Z"}, {"entity": "publication", "iuid": "7f1ea59b281c4f869a2b8e7a6dc5d6dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f1ea59b281c4f869a2b8e7a6dc5d6dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f1ea59b281c4f869a2b8e7a6dc5d6dd"}}, "title": "Decoding murine corneal epithelial specification and homeostasis by single-cell spatial transcriptomics with scRNA-seq enrichment", "authors": [{"family": "Javidjam", "given": "Dina", "initials": "D", "orcid": "0000-0003-4436-5928", "researcher": {"href": "https://publications.scilifelab.se/researcher/69cc19a0f07b4e16a33bb9ff5114eced.json"}}, {"family": "Vattulainen", "given": "Meri", "initials": "M", "orcid": "0000-0003-1343-1232", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c70e5d8ac9b418bbfd25c851492716e.json"}}, {"family": "Lagali", "given": "Neil", "initials": "N", "orcid": "0000-0003-1079-4361", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6d3fe5278714b4784551cdcc8166aa1.json"}}, {"family": "Moustardas", "given": "Petros", "initials": "P", "orcid": "0000-0003-3192-3708", "researcher": {"href": "https://publications.scilifelab.se/researcher/eddb470abb044abebf415daa656c77df.json"}}], "type": "posted-content", "published": "2026-05-12", "journal": {"issn-l": null}, "abstract": null, "doi": "10.64898/2026.05.08.723186", "pmid": null, "labels": {"Clinical Genomics": "Service", "Clinical Genomics Link\u00f6ping": "Service"}, "xrefs": [], "notes": [], "created": "2026-05-19T07:32:34.862Z", "modified": "2026-05-19T07:33:05.587Z"}, {"entity": "publication", "iuid": "f74db641b67b4485b01bf07e453d5dd0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f74db641b67b4485b01bf07e453d5dd0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f74db641b67b4485b01bf07e453d5dd0"}}, "title": "Draft assemblies for 177 bird species enhance genus-level coverage.", "authors": [{"family": "Chen", "given": "Guangji", "initials": "G", "orcid": "0000-0002-9441-1155", "researcher": {"href": "https://publications.scilifelab.se/researcher/19514f67b1504dc6b4b7d393e97f8cc0.json"}}, {"family": "Wang", "given": "Shuang", "initials": "S", "orcid": "0009-0008-9451-5684", "researcher": {"href": "https://publications.scilifelab.se/researcher/186a6001c26a403e8b0640a3cb516a1a.json"}}, {"family": "Bilyeli \u00d8ksnebjerg", "given": "Daniel", "initials": "D"}, {"family": "Nielsen", "given": "Sascha Dreyer", "initials": "SD", "orcid": "0000-0003-2485-9314", "researcher": {"href": "https://publications.scilifelab.se/researcher/70ff8708bff74ea4b0c80c5f434329a8.json"}}, {"family": "Dai", "given": "Wei", "initials": "W", "orcid": "0000-0001-9286-759X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7c48f0de21d478ab23bc18b439472e0.json"}}, {"family": "Jiang", "given": "Wei", "initials": "W"}, {"family": "Liang", "given": "Jing", "initials": "J"}, {"family": "Han", "given": "Wei", "initials": "W"}, {"family": "Zhou", "given": "Chengran", "initials": "C", "orcid": "0000-0002-9468-5973", "researcher": {"href": "https://publications.scilifelab.se/researcher/49d36e1d73bb440184212119bf82858c.json"}}, {"family": "Li", "given": "Qiye", "initials": "Q", "orcid": "0000-0002-5993-0312", "researcher": {"href": "https://publications.scilifelab.se/researcher/d807a3a13669425c9b00e4a2b7db672a.json"}}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Monadjem", "given": "Ara", "initials": "A", "orcid": "0000-0003-1906-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/94671b1f708d49f5b9eebc0e6b78b82e.json"}}, {"family": "Bhembe", "given": "Zamekile D", "initials": "ZD", "orcid": "0009-0006-5354-5751", "researcher": {"href": "https://publications.scilifelab.se/researcher/d276b65085fa48bdb17d12ecb8b014ac.json"}}, {"family": "Maphalala", "given": "Machawe", "initials": "M", "orcid": "0000-0002-9304-1391", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eebd8acec5a4084b64c3be4a3627b67.json"}}, {"family": "Ocampo", "given": "Diego", "initials": "D"}, {"family": "Sandoval", "given": "Luis", "initials": "L", "orcid": "0000-0002-0793-6747", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8f560d617c2432aa26f9700d2311ac1.json"}}, {"family": "Fickel", "given": "J\u00f6rns", "initials": "J", "orcid": "0000-0002-0593-5820", "researcher": {"href": "https://publications.scilifelab.se/researcher/40018134351a481ab2d00b4113404c47.json"}}, {"family": "Greenwood", "given": "Alex D", "initials": "AD", "orcid": "0000-0002-8249-1565", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab62cca19d7641918b6dd9adbff919c5.json"}}, {"family": "Szentiks", "given": "Claudia A", "initials": "CA"}, {"family": "Roller", "given": "Marco", "initials": "M"}, {"family": "Birks", "given": "Sharon M", "initials": "SM"}, {"family": "Leach\u00e9", "given": "Adam D", "initials": "AD", "orcid": "0000-0001-8929-6300", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c9502316d344a1282bec0f444638222.json"}}, {"family": "Rico-Guevara", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-4067-5312", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe305adf4d234dce94a9c74ca873169d.json"}}, {"family": "Fuchs", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Vy", "given": "Nguyen Tran", "initials": "NT"}, {"family": "Hvilsom", "given": "Christina", "initials": "C", "orcid": "0000-0001-7870-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/19e68386a9414dad9162026abafad7ce.json"}}, {"family": "Berner", "given": "Juliana Andrea", "initials": "JA"}, {"family": "Lifjeld", "given": "Jan Terje", "initials": "JT"}, {"family": "Johnsen", "given": "Arild", "initials": "A", "orcid": "0000-0003-4864-6284", "researcher": {"href": "https://publications.scilifelab.se/researcher/d610052c8e134f9a9ddff3eee7ed864d.json"}}, {"family": "Johannessen", "given": "Lars Erik", "initials": "LE", "orcid": "0000-0001-5981-9190", "researcher": {"href": "https://publications.scilifelab.se/researcher/838c1d1eb4bb4861a2408a5d83b616cb.json"}}, {"family": "Labuschagne", "given": "Kim", "initials": "K", "orcid": "0000-0003-2784-4767", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfa0e1dbf2194c5bbcfb36769d1b2cf4.json"}}, {"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Reeve", "given": "Andrew Hart", "initials": "AH"}, {"family": "Joseph", "given": "Leo", "initials": "L", "orcid": "0000-0001-7564-1978", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a0b6c400914ba9aaca4a51587d1893.json"}}, {"family": "Hellgren", "given": "Olof", "initials": "O"}, {"family": "Brumfield", "given": "Robb T", "initials": "RT", "orcid": "0000-0003-2307-0688", "researcher": {"href": "https://publications.scilifelab.se/researcher/71a3a36f83154d3dbe14e1a5290f425f.json"}}, {"family": "Burg", "given": "Theresa M", "initials": "TM", "orcid": "0000-0001-5096-3479", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab837fec0ea64df5bd66001038f505c5.json"}}, {"family": "Illera", "given": "Juan Carlos", "initials": "JC", "orcid": "0000-0002-4389-0264", "researcher": {"href": "https://publications.scilifelab.se/researcher/d137c193d3cd4f8c8b9fe09a6443033c.json"}}, {"family": "Aleixo", "given": "Alexandre", "initials": "A", "orcid": "0000-0002-7816-9725", "researcher": {"href": "https://publications.scilifelab.se/researcher/b397ed6da07246caa50a438c233820ab.json"}}, {"family": "Smit", "given": "Ben", "initials": "B"}, {"family": "Rheindt", "given": "Frank E", "initials": "FE", "orcid": "0000-0001-8946-7085", "researcher": {"href": "https://publications.scilifelab.se/researcher/744276ae56e24e7295f672854fbaf3d9.json"}}, {"family": "Lee", "given": "Jessica", "initials": "J", "orcid": "0000-0003-0757-4237", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ec08a3cbe214f22b05c730bf94613aa.json"}}, {"family": "Nishiumi", "given": "Isao", "initials": "I"}, {"family": "Quesada", "given": "Javier", "initials": "J", "orcid": "0000-0002-6010-8473", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c4e889bf2fd424c915c6487038f7950.json"}}, {"family": "Dumbacher", "given": "John P", "initials": "JP"}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a043d6f016b46709ace7f181d8cd3b8.json"}}, {"family": "Andersen", "given": "Michael J", "initials": "MJ", "orcid": "0000-0002-7220-5588", "researcher": {"href": "https://publications.scilifelab.se/researcher/15d3b310f2f34fc4969520d431a14f6d.json"}}, {"family": "Witt", "given": "Christopher C", "initials": "CC", "orcid": "0000-0003-2781-1543", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a6a535b32f94e59acf1398df72a8cd1.json"}}, {"family": "Phillips", "given": "Richard A", "initials": "RA", "orcid": "0000-0002-0208-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/f35746710d7c4ae6a86d1b12e805ea14.json"}}, {"family": "Prum", "given": "Richard", "initials": "R", "orcid": "0000-0002-4741-7132", "researcher": {"href": "https://publications.scilifelab.se/researcher/28d15772cf924924b7e5630bfbdb5b89.json"}}, {"family": "Zyskowski", "given": "Kristof", "initials": "K", "orcid": "0000-0002-5680-6412", "researcher": {"href": "https://publications.scilifelab.se/researcher/49aadb5fab7b4fbebf1c65c9f3a04217.json"}}, {"family": "Goodman", "given": "Steven M", "initials": "SM"}, {"family": "Raherilalao", "given": "Marie Jeanne", "initials": "MJ", "orcid": "0000-0002-8618-7157", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5653450df494d96b15d77a12d77e932.json"}}, {"family": "Ottosson", "given": "Ulf", "initials": "U", "orcid": "0000-0001-7914-0484", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b035efe180248eaa188b0e1d23f2007.json"}}, {"family": "Barshep", "given": "Yahkat", "initials": "Y"}, {"family": "Ivande", "given": "Sam", "initials": "S", "orcid": "0000-0003-4949-1376", "researcher": {"href": "https://publications.scilifelab.se/researcher/181e4fbbf6ae40d1bebe504c5c24f797.json"}}, {"family": "Brl\u00edk", "given": "Vojt\u011bch", "initials": "V", "orcid": "0000-0002-7902-8123", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ed62d45f978413d9c983e53b07b7ad8.json"}}, {"family": "Okposio", "given": "Emmanuel", "initials": "E"}, {"family": "Koane", "given": "Bonny", "initials": "B", "orcid": "0000-0001-6770-5126", "researcher": {"href": "https://publications.scilifelab.se/researcher/966dc22dd4ca456294f7f2ed0a853c87.json"}}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Rahbek", "given": "Carsten", "initials": "C", "orcid": "0000-0003-4585-0300", "researcher": {"href": "https://publications.scilifelab.se/researcher/341ee33c55904249b6e70a9b55b5509a.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F", "orcid": "0000-0001-9920-8167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e9cc44c016c4d099f674d182c08fbaa.json"}}, {"family": "Graves", "given": "Gary R", "initials": "GR", "orcid": "0000-0003-1406-5246", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc3b9edee185456d971f5b596c3086fe.json"}}, {"family": "Feng", "given": "Shaohong", "initials": "S", "orcid": "0000-0002-2462-7348", "researcher": {"href": "https://publications.scilifelab.se/researcher/92ad360b09004877aee9cfde491c76a3.json"}}, {"family": "Hosner", "given": "Peter A", "initials": "PA", "orcid": "0000-0001-7499-6224", "researcher": {"href": "https://publications.scilifelab.se/researcher/87a4c8cd6229436d9a39761aa77eeec2.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}], "type": "journal article", "published": "2026-05-09", "journal": {"title": "Gigascience", "issn": "2047-217X", "issn-l": "2047-217X"}, "abstract": "With over 10,000 recognized species, birds constitute one of the most diverse and widely distributed vertebrate groups. Although avian genomics has advanced rapidly over the past decade, substantial gaps remain across the global avifauna. Filling these gaps is essential for understanding macroevolutionary patterns, population structure, and the molecular basis of ecological and behavioral diversity. Worldwide museum collections represent invaluable resources for filling these gaps, yet the typically degraded DNA and limited quantities from historical specimens have posed significant challenges for generating high-quality genome assemblies.\n\nHere, the Bird Genome 10 K (B10K) Project adopted low-input sequencing strategies that reduce costs while improving assembly quality compared with earlier order- and family-level genomes. Using mainly stLFR, complemented by 10X Genomics and standard next-generation sequencing, we assembled 177 avian genomes from museum specimens and tissue collections representing 161 genera, including 102 newly sequenced at the genomic level. The assemblies average \u223c1.2 Gb in size, with scaffold N50 = 8.03 Mb, contig N50 = 120 kb, 93% BUSCO completeness, and Merqury QV score of 56.\n\nThese genomes greatly expand avian taxonomic coverage and demonstrate the efficiency of low-input sequencing for generating high-quality assemblies from limited and often degraded material sourced from museum specimens. This resource provides a foundation for comparative genomics, conservation genetics, and evolutionary studies across the avian tree of life.", "doi": "10.1093/gigascience/giag045", "pmid": "42104960", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "8675036"}], "notes": [], "created": "2026-06-08T17:18:43.899Z", "modified": "2026-06-08T17:18:48.101Z"}, {"entity": "publication", "iuid": "b09b02fc5fff4122883cede0ca76ddbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b09b02fc5fff4122883cede0ca76ddbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b09b02fc5fff4122883cede0ca76ddbf"}}, "title": "Mitochondria serve as a holdout compartment for aggregation-prone proteins hindering efficient degradation.", "authors": [{"family": "Gierisch", "given": "Maria E", "initials": "ME", "orcid": "0000-0002-8053-4402", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe10e1b3af59418a8edbd1fea8c37faf.json"}}, {"family": "Barchi", "given": "Enrica", "initials": "E", "orcid": "0009-0007-3209-0003", "researcher": {"href": "https://publications.scilifelab.se/researcher/87a02a6f87294bbd96c11b502f5fba1c.json"}}, {"family": "Marogna", "given": "Mirco", "initials": "M", "orcid": "0009-0000-9866-470X", "researcher": {"href": "https://publications.scilifelab.se/researcher/61ea01f03c4b4995af9e91481cedc783.json"}}, {"family": "Walln\u00f6fer", "given": "Moritz H", "initials": "MH", "orcid": "0000-0002-7688-2359", "researcher": {"href": "https://publications.scilifelab.se/researcher/26832fc473694946b8cd60b280b2a78d.json"}}, {"family": "Ankarcrona", "given": "Maria", "initials": "M", "orcid": "0000-0002-7022-3694", "researcher": {"href": "https://publications.scilifelab.se/researcher/5deb5cb7c18647b5b37d80221b67086c.json"}}, {"family": "Naia", "given": "Luana", "initials": "L", "orcid": "0000-0002-0886-4634", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6ae78f608af4f3f8524d5ab4a3c6cdd.json"}}, {"family": "Salomons", "given": "Florian A", "initials": "FA"}, {"family": "Dantuma", "given": "Nico P", "initials": "NP", "orcid": "0000-0002-6090-4170", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ccdd02c787d4a699efd24d297040aa0.json"}}], "type": "journal article", "published": "2026-05-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "17", "issue": "1", "pages": null}, "abstract": "The accumulation of protein aggregates has been causatively linked to the pathogenesis of neurodegenerative diseases. Here, we conduct a genome-wide CRISPR-Cas9 screen to identify cellular factors that regulate the degradation of an aggregation-prone reporter. Genes encoding proteins involved in mitochondrial homeostasis, including the translation factor eIF5A, are enriched among suppressors of the degradation of the reporter. Genetic or chemical inhibition of eIF5A leads to dissociation of the aggregation-prone substrate from mitochondria, which is accompanied by enhanced ubiquitin-dependent proteasomal degradation. The presence of an aggregation-prone, amphipathic helix that localizes the reporter to mitochondria is crucial for the stimulatory effect of eIF5A inhibition on proteasomal degradation. Additionally, inhibition of eIF5A also enhances degradation of mutant huntingtin and \u03b1-synuclein, two disease-associated proteins that contain amphipathic helices and mislocalize to mitochondria. We propose that mitochondria serve as a holdout compartment for aggregation-prone proteins. Therefore, preventing mitochondrial localization of aggregation-prone proteins may offer a viable therapeutic strategy for reducing disease-associated proteins in neurodegenerative disorders.", "doi": "10.1038/s41467-026-72783-0", "pmid": "42098118", "labels": {"CRISPR Functional Genomics": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13153185"}, {"db": "pii", "key": "10.1038/s41467-026-72783-0"}], "notes": [], "created": "2026-05-11T12:46:18.151Z", "modified": "2026-06-08T19:20:13.544Z"}, {"entity": "publication", "iuid": "59d7ae58ceea4c3bb2eb1e766d18641a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59d7ae58ceea4c3bb2eb1e766d18641a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59d7ae58ceea4c3bb2eb1e766d18641a"}}, "title": "Spatiotemporal analysis reveals distinct inflammatory programs underlying chronic colitis.", "authors": [{"family": "Fransson", "given": "Jennifer", "initials": "J"}, {"family": "Sorini", "given": "Chiara", "initials": "C"}, {"family": "Castillo", "given": "Francisca", "initials": "F"}, {"family": "Chi", "given": "Yuhao", "initials": "Y"}, {"family": "He", "given": "Ning", "initials": "N"}, {"family": "Suarez-Alvarez", "given": "Martin", "initials": "M"}, {"family": "Ulloa", "given": "Maria Alejandra", "initials": "MA"}, {"family": "Morales Castro", "given": "Rodrigo A", "initials": "RA"}, {"family": "Okhovat", "given": "Ali", "initials": "A"}, {"family": "Sounart", "given": "Hailey", "initials": "H"}, {"family": "Zagami", "given": "Chiara", "initials": "C"}, {"family": "Cardoso", "given": "Rebeca F", "initials": "RF"}, {"family": "Das", "given": "Srustidhar", "initials": "S"}, {"family": "Giacomello", "given": "Stefania", "initials": "S"}, {"family": "Mechling", "given": "Anna", "initials": "A"}, {"family": "Hedin", "given": "Charlotte R H", "initials": "CRH"}, {"family": "Smith", "given": "Philip", "initials": "P"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ"}], "type": "journal article", "published": "2026-05-06", "journal": {"title": "Immunity", "issn": "1097-4180", "issn-l": "1074-7613"}, "abstract": "Inflammatory bowel disease (IBD) is a complex disorder that is often resistant to immunomodulatory treatments. Here, to understand how immune, epithelial, and stromal compartments are rewired during disease initiation and progression, we leveraged T cell transfer and Il10-/- spontaneous colitis models, including anti-IL-12p40 intervention, and integrated time-course transcriptomic analyses at bulk, single-cell, and spatial resolution. These well-established models exhibited conserved features of chronic inflammation, including neutrophil infiltration, and impaired tissue regeneration. Comparison of murine transcriptional programs and human IBD datasets revealed neutrophil-associated inflammation and cytokine signaling as the most conserved pathways across species. We identified spatial heterogeneity in inflammatory modules and described three gene programs with differential spatial and temporal distributions, including one corresponding to tertiary lymphoid structures. When used together, these models recapitulate complementary aspects of human disease at both cellular and transcriptional levels. This high-resolution spatiotemporal atlas will guide future translational research aimed at optimizing therapeutic strategies for IBD.", "doi": "10.1016/j.immuni.2026.04.005", "pmid": "42097141", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S1074-7613(26)00167-6"}], "notes": [], "created": "2026-05-11T11:50:48.709Z", "modified": "2026-05-11T11:50:48.717Z"}, {"entity": "publication", "iuid": "e7038b6561ed4a8282747388827a8dac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7038b6561ed4a8282747388827a8dac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7038b6561ed4a8282747388827a8dac"}}, "title": "Neuroinflammation and neurodegeneration trigger a specific splice form of ribosomal protein S24.", "authors": [{"family": "Magadi", "given": "Srivathsa S", "initials": "SS"}, {"family": "Jonson", "given": "Maria", "initials": "M"}, {"family": "Lucena", "given": "Pablo B", "initials": "PB"}, {"family": "Caliandro", "given": "Michele F", "initials": "MF"}, {"family": "Almeida", "given": "Beatriz", "initials": "B"}, {"family": "Bilalli", "given": "Lorina", "initials": "L"}, {"family": "Budinger", "given": "Dimitri", "initials": "D", "orcid": "0000-0001-7002-1091", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecc1d3189e714b89a58b392e2a05eb8e.json"}}, {"family": "Tsoi", "given": "Anna", "initials": "A"}, {"family": "Ntzouni", "given": "Maria", "initials": "M"}, {"family": "Maqdissi", "given": "Joseph Agi", "initials": "JA"}, {"family": "Kaczmarczyk", "given": "Lech", "initials": "L"}, {"family": "Zijlstra", "given": "Jente J", "initials": "JJ"}, {"family": "Faketija", "given": "Matej", "initials": "M"}, {"family": "Perkins", "given": "Matthew", "initials": "M"}, {"family": "Paul", "given": "Gesine", "initials": "G"}, {"family": "Hallbeck", "given": "Martin", "initials": "M", "orcid": "0000-0001-6716-0314", "researcher": {"href": "https://publications.scilifelab.se/researcher/17f7b361871045a1b1e3cdfec9ebe5ec.json"}}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Watts", "given": "Joel C", "initials": "JC"}, {"family": "Reichenbach", "given": "Nicole", "initials": "N"}, {"family": "Petzold", "given": "Gabor C", "initials": "GC", "orcid": "0000-0002-0145-8641", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a64d37850384e10a8a4199ea81ae856.json"}}, {"family": "Schieweck", "given": "Rico", "initials": "R"}, {"family": "Heneka", "given": "Michael T", "initials": "MT", "orcid": "0000-0003-4996-1630", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c46f161bc8544a78eef05ee0b74bb47.json"}}, {"family": "Jackson", "given": "Walker S", "initials": "WS"}], "type": "journal article", "published": "2026-05-06", "journal": {"title": "Brain", "issn": "1460-2156", "issn-l": "0006-8950"}, "abstract": "Neuroinflammation, particularly that involving reactive microglia, the brain's resident immune cells, is implicated in the pathogenesis of major neurodegenerative diseases (NDs). Multiple studies have reported changes in ribosomal protein (RP) expression during neurodegeneration, but the significance of these changes remains unclear. Ribosomes are evolutionarily conserved protein-synthesizing machines, and although commonly viewed as invariant, accumulating evidence suggests functional ribosome specialization through variation in their protein composition. Among RPs, S24, encoded by RPS24 in humans and Rps24 in mice, is unique as its transcripts undergo alternative splicing to produce protein variants with different C-terminal sequences that are differentially expressed across tissues and cell types. Understanding heterogeneous RP expression patterns across brain regions and cell types could reveal mechanisms underlying selective vulnerability in NDs and provide new biomarkers for neuroinflammatory responses. To identify RP expression patterns across brain regions in neurons, astrocytes, and microglia we analyzed cell type-specific translating mRNAs from mice. To investigate Rps24 isoform-specific expression, we performed cell type-resolved transcript analysis and developed antibodies specific for the S24-PKE protein variant encoded by mRNA isoform Rps24c. We examined Rps24c/S24-PKE expression in brains from mouse models of aging and neurodegeneration, as well as in human postmortem tissue from patients with Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). This work revealed distinct RP expression patterns across brain regions and between neurons, astrocytes, and microglia, including neuron-enriched RPs Rpl13a and Rps10. Analysis of RP paralogs revealed complex expression relationships with their canonical counterparts, suggesting regulated mechanisms for generating heterogeneous ribosomes. Across brain regions and cell types, Rplp0 and Rpl13a, commonly used normalization references, showed heterogeneous expression, raising important methodological considerations for gene expression studies. Rps24 isoforms exhibited striking cell type-specific expression patterns. Rps24c was predominantly expressed in microglia and was increased by neuroinflammation caused by aging, neurodegeneration, or inflammatory chemicals. Using S24-PKE-specific antibodies, we verified increased expression of this protein variant in brains with AD, PD, and HD, and in relevant mouse models. These findings establish heterogeneous RP expression as a feature of brain cell types which may enable cell type-specific translation regulation via specialized ribosomes. This work also identifies Rps24c/S24-PKE as a potential novel marker for neuroinflammation and neurodegeneration and provides new tools for monitoring these responses.", "doi": "10.1093/brain/awag166", "pmid": "42087813", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "8670210"}], "notes": [], "created": "2026-05-11T12:23:19.422Z", "modified": "2026-05-11T12:23:19.728Z"}, {"entity": "publication", "iuid": "0b5724836e6f4770bb25d06ab0e11807", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b5724836e6f4770bb25d06ab0e11807.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b5724836e6f4770bb25d06ab0e11807"}}, "title": "Ribosome dynamics during skeletal muscle repair and regeneration in mice and humans.", "authors": [{"family": "Cui", "given": "Minying", "initials": "M"}, {"family": "Edman", "given": "Sebastian", "initials": "S", "orcid": "0000-0003-2921-833X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d00d020f7c84efa845fe368e7214130.json"}}, {"family": "Jude", "given": "Baptiste", "initials": "B", "orcid": "0000-0002-5506-2482", "researcher": {"href": "https://publications.scilifelab.se/researcher/60e0f4af135c4eff99a95ff1cac825bb.json"}}, {"family": "Jannig", "given": "Paulo R", "initials": "PR"}, {"family": "Horwath", "given": "Oscar", "initials": "O", "orcid": "0000-0002-3500-2896", "researcher": {"href": "https://publications.scilifelab.se/researcher/99970942c0114dd68a34a0524e6b5748.json"}}, {"family": "Shorter", "given": "Emily", "initials": "E"}, {"family": "Koopmans", "given": "Pieter J", "initials": "PJ", "orcid": "0000-0002-4797-5265", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4f437cb611e4327a33133c3e415c6e8.json"}}, {"family": "Chambers", "given": "Toby L", "initials": "TL", "orcid": "0000-0001-7567-1819", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ece3fb9212d4e309858701afb620180.json"}}, {"family": "Jones", "given": "Ronald G", "initials": "RG"}, {"family": "Nilsson", "given": "Abraham", "initials": "A"}, {"family": "Lanner", "given": "Johanna T", "initials": "JT", "orcid": "0000-0002-1222-9473", "researcher": {"href": "https://publications.scilifelab.se/researcher/d502479c111b4bec884fd275c2ce6384.json"}}, {"family": "Sejersen", "given": "Thomas", "initials": "T", "orcid": "0000-0001-5961-7097", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab13ad6b63424037addb7dd1afbda3b2.json"}}, {"family": "Pont\u00e9n", "given": "Eva", "initials": "E", "orcid": "0000-0001-5228-1914", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9bf1a45788a4e34be6734ce15d9de5d.json"}}, {"family": "Murach", "given": "Kevin A", "initials": "KA", "orcid": "0000-0003-2783-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/76f498f06fa0451e97123a8d5a333820.json"}}, {"family": "Schilcher", "given": "J\u00f6rg", "initials": "J"}, {"family": "von Walden", "given": "Ferdinand", "initials": "F", "orcid": "0000-0003-1134-2252", "researcher": {"href": "https://publications.scilifelab.se/researcher/903e0b7523da4a49960e677009942f67.json"}}], "type": "journal article", "published": "2026-05-01", "journal": {"title": "Am. J. Physiol., Cell Physiol.", "issn": "1522-1563", "issn-l": "0363-6143"}, "abstract": "Skeletal muscle repair requires coordinated regulation of inflammation and protein synthesis, but the roles of ribosome biogenesis and protein composition remain poorly defined. To address this, mice underwent femoral artery ligation (FAL) to induce muscle regeneration over 28 days. In humans, tibialis anterior biopsies from traumatic tibial fracture patients were subjected to RNA sequencing. Following FAL, c-Myc mRNA increased transiently, followed by increased ribosomal DNA transcription, leading to elevated total RNA levels. Skeletal muscle-specific ribosomal protein paralog RPL3L was replaced by the ubiquitously expressed RPL3 during the initial phases of recovery, but this shift was reversed by day 28. A substantial transcriptomic response was observed in human muscle injury, with heavy emphasis on MYC-induced anabolism and inflammation. This supports a model in which MYC-driven changes in ribosomal content and composition form a core anabolic module in skeletal muscle repair, potentially representing a targetable axis to enhance recovery after muscle injury.", "doi": "10.1152/ajpcell.00184.2026", "pmid": "42065367", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-05-11T12:28:52.694Z", "modified": "2026-05-11T12:28:53.459Z"}, {"entity": "publication", "iuid": "8c4aba44bdff437e978cbca1070e66d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8c4aba44bdff437e978cbca1070e66d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8c4aba44bdff437e978cbca1070e66d2"}}, "title": "Process development and pilot-scale validation of \u03b3-valerolactone pretreatment for softwood biorefining", "authors": [{"family": "Dixit", "given": "Pooja", "initials": "P", "orcid": "0009-0008-8836-0612", "researcher": {"href": "https://publications.scilifelab.se/researcher/b137569ea7a341a8a7df72b986e422fa.json"}}, {"family": "Benavente", "given": "Ver\u00f3nica", "initials": "V", "orcid": "0000-0003-3252-467X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00aa585064134a88888885c3f0b8ee7f.json"}}, {"family": "Gustafsson", "given": "Tomas", "initials": "T"}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M", "orcid": "0000-0002-0903-6662", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db0f81a369741b0847c6f79746d82aa.json"}}, {"family": "Gorzs\u00e1s", "given": "Andr\u00e1s", "initials": "A", "orcid": "0000-0002-2298-8844", "researcher": {"href": "https://publications.scilifelab.se/researcher/8070792ccead4c809c89943d84cf0e03.json"}}, {"family": "Sundman", "given": "Ola", "initials": "O", "orcid": "0000-0002-1705-5249", "researcher": {"href": "https://publications.scilifelab.se/researcher/c15a15210b8a41e0826343602778bc6d.json"}}, {"family": "Romero-Soto", "given": "Luis A", "initials": "LA", "orcid": "0000-0001-7409-1943", "researcher": {"href": "https://publications.scilifelab.se/researcher/b821f6cfff6240b78db89ac843df7b1b.json"}}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ", "orcid": "0000-0003-3866-0111", "researcher": {"href": "https://publications.scilifelab.se/researcher/1769e674df8649ce82a0d058f0a309dc.json"}}, {"family": "Mart\u00edn", "given": "Carlos", "initials": "C", "orcid": "0000-0002-4258-0512", "researcher": {"href": "https://publications.scilifelab.se/researcher/7300805a6af44b9687438bb882be7e71.json"}}], "type": "journal-article", "published": "2026-05-00", "journal": {"title": "Biomass and Bioenergy", "issn": "0961-9534", "volume": "208", "pages": "108846", "issn-l": null}, "abstract": null, "doi": "10.1016/j.biombioe.2025.108846", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-02-20T12:59:26.566Z", "modified": "2026-02-20T12:59:27.361Z"}, {"entity": "publication", "iuid": "9e4daf0046b8477fbc62333829667614", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e4daf0046b8477fbc62333829667614.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e4daf0046b8477fbc62333829667614"}}, "title": "Epigenetic changes as regulatory mechanism for the expression of life history stages in Zonotrichia capensis inhabiting an aseasonal environment", "authors": [{"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F", "orcid": "0000-0002-7214-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}}, {"family": "Gonzalez\u2010 Gomez", "given": "Paulina L", "initials": "PL", "orcid": "0000-0002-1219-8881", "researcher": {"href": "https://publications.scilifelab.se/researcher/636c42cfcc1f46c4bc83ffaa6f99c597.json"}}, {"family": "Wingfield", "given": "John C", "initials": "JC"}, {"family": "Guerrero\u2010Bosagna", "given": "Carlos", "initials": "C", "orcid": "0000-0003-1935-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/0175a0da7ca147d4a0430b085ed23669.json"}}], "type": "journal-article", "published": "2026-05-00", "journal": {"title": "Journal of Avian Biology", "issn": "0908-8857", "volume": "2026", "issue": "3", "issn-l": null}, "abstract": null, "doi": "10.1002/jav.03516", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-06-01T11:10:53.812Z", "modified": "2026-06-01T11:10:54.000Z"}, {"entity": "publication", "iuid": "3c879540016f423ca84894bb30eae1b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3c879540016f423ca84894bb30eae1b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3c879540016f423ca84894bb30eae1b5"}}, "title": "Machine learning based multi-omics analysis reveals key molecular determinants of Parkinson's disease severity.", "authors": [{"family": "Jin", "given": "Han", "initials": "H"}, {"family": "Meng", "given": "Lingqi", "initials": "L"}, {"family": "Yulug", "given": "Burak", "initials": "B"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Cankaya", "given": "Seyda", "initials": "S"}, {"family": "Hanoglu", "given": "Lutfu", "initials": "L"}, {"family": "Ji", "given": "Boyu", "initials": "B"}, {"family": "Coskun", "given": "Ebru", "initials": "E"}, {"family": "Idil", "given": "Ezgi", "initials": "E"}, {"family": "Nogaylar", "given": "Rahim", "initials": "R"}, {"family": "Oktem", "given": "Ece Ozdemir", "initials": "EO"}, {"family": "Sayman", "given": "Dila", "initials": "D"}, {"family": "Karaca", "given": "Ramazan", "initials": "R"}, {"family": "Ozsimsek", "given": "Ahmet", "initials": "A"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2026-04-30", "journal": {"title": "Neurobiol. Dis.", "issn": "1095-953X", "volume": "225", "pages": "107424", "issn-l": "0969-9961"}, "abstract": "While single-omics analyses of Parkinson's Disease (PD) have demonstrated their ability in revealing the underlying molecular mechanisms, they often fail to provide a comprehensive view of the complete disease mechanisms. In this study, we leveraged multi-omics data from 64 heterogeneous, well-phenotyped PD patients, generated plasma metabolomics data and Olink proteomics data together with the gut and saliva metagenomics data, and investigated the altered molecular mechanisms and their interactions in association with the severity of motor function disorders in PD patients. Based on our multi-omics approach, we identified a panel of 58 biomarkers comprising one clinical variable, 10 proteins, and 17 metabolites from plasma, 26 gut species, and 4 saliva species for PD severity. These biomarkers exhibited superior predictive performance for assessing PD severity compared to those derived from single-omics datasets. The predictive power of our machine learning models based on these biomarkers was validated using additional multi-omics data from the same group of PD patients after a 3-month follow-up. The contribution of each omics dataset was evaluated by both supervised and unsupervised machine learning approaches, highlighting the importance of plasma metabolomics in disease stratification. Our study unveiled disease-related molecular alterations across multiple omics datasets, offering potential diagnostic and therapeutic insights for PD. Moreover, it underpinned the significance of employing multi-omics analyses when studying complex diseases like PD.", "doi": "10.1016/j.nbd.2026.107424", "pmid": "42069091", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0969-9961(26)00169-5"}], "notes": [], "created": "2026-05-11T11:43:55.203Z", "modified": "2026-05-11T11:43:55.359Z"}, {"entity": "publication", "iuid": "b87ff717143c4bf38090dc1906217558", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b87ff717143c4bf38090dc1906217558.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b87ff717143c4bf38090dc1906217558"}}, "title": "Divergent cis-regulatory haplotypes at Tlr2 are associated with immune responsiveness.", "authors": [{"family": "Nandakumar", "given": "Mridula", "initials": "M"}, {"family": "Lundberg", "given": "Max", "initials": "M"}, {"family": "Nouri", "given": "Mehrnaz", "initials": "M"}, {"family": "Valfridsson", "given": "Christine", "initials": "C"}, {"family": "Carlsson", "given": "Fredric", "initials": "F"}, {"family": "R\u00e5berg", "given": "Lars", "initials": "L", "orcid": "0000-0001-5219-7448", "researcher": {"href": "https://publications.scilifelab.se/researcher/a732076e5acc4ede94cc864cd90c99f3.json"}}], "type": "journal article", "published": "2026-04-29", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038"}, "abstract": "Positive and balancing selection on pattern recognition receptors (PRRs) is widely thought to target ligand-binding domains and affect the specificity of recognition of different pathogens. Alternatively, positive/balancing selection on PRRs could affect general responsiveness by targeting for example signaling domains or cis-regulatory variation. Studies of a wild rodent (the bank vole, Clethrionomys glareolus) have shown that Tlr2-a lipoprotein-binding PRR-is highly polymorphic with divergent haplotypes and signatures of balancing selection, and that Tlr2 genotype is associated with susceptibility to Borrelia afzelii infection in the wild. To investigate what aspect of Tlr2 function has been under selection, we here perform integrated population genetic and functional analyses. Ex vivo infection experiments show that the protective Tlr2 haplotype produces a stronger proinflammatory response to B. afzelii compared to the haplotype associated with susceptibility. Tlr2 genotype has a similar, albeit not statistically significant, effect on responsiveness to the phylogenetically distant pathogen Streptococcus pyogenes. We find that the strongest signature of balancing selection is 4.6 kb upstream of the Tlr2 coding sequence, near a putative enhancer, and that Tlr2 exhibits allele-specific expression such that the protective haplotype is more expressed. Collectively these results indicate that balancing selection has primarily acted on cis-regulatory variation affecting the general responsiveness via Tlr2-signaling rather than on polymorphisms affecting Tlr2 ligand-binding specificity.", "doi": "10.1093/molbev/msag113", "pmid": "42052896", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "8664598"}], "notes": [], "created": "2026-05-11T11:52:59.250Z", "modified": "2026-05-11T11:52:59.327Z"}, {"entity": "publication", "iuid": "192bc0ba645d4a9babc3be3256ac2d23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/192bc0ba645d4a9babc3be3256ac2d23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/192bc0ba645d4a9babc3be3256ac2d23"}}, "title": "Breeding for climate adaptation: genetic variation and genomic selection for drought response in Scots pine.", "authors": [{"family": "Chaudhary", "given": "Rajiv", "initials": "R"}, {"family": "Estravis Barcala", "given": "Maximiliano", "initials": "M"}, {"family": "Fundova", "given": "Irena", "initials": "I"}, {"family": "Funda", "given": "Tomas", "initials": "T"}, {"family": "Chen", "given": "Zhi-Qiang", "initials": "ZQ"}, {"family": "Wu", "given": "Harry X", "initials": "HX"}], "type": "journal article", "published": "2026-04-27", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "27", "issue": "1", "issn-l": "1471-2164"}, "abstract": "Drought intensity and frequency are increasing under global warming in the boreal forests, and breeding for drought resistance will facilitate adaptation of new planting material to changing climate conditions. We used a tree-ring dataset of 559 individuals to study Scots pine genetic variation and the efficiency of genomic selection of drought-response traits (drought resistance, recovery and resilience), for the first time. From genotyping-by-sequencing (GBS), 31,101 SNPs were generated and used for the study.\n\nSignificant genetic variation was detected for drought-response and other growth, wood-anatomy and wood density traits. Heritability estimates for wood-anatomical traits were higher than those for drought-response and growth traits. Genetic correlations between drought-response and wood-anatomical traits were generally high but mostly nonsignificant. In contrast, drought resistance and recovery showed positive and significant correlations with basal area increment and height. We found that the predictive ability and accuracy for drought-response traits were lower than those for wood-anatomical traits, and were comparable between GBLUP and ABLUP. Greater genetic gain per year can be achieved through genomic selection relative to pedigree-based selection if the generation interval is reduced.\n\nThe positive genetic correlation between drought-response and growth traits will enable simultaneous selection for improved growth and increased drought resistant trees in Scots pine breeding through either pedigreed-based and genomic selection.\n\nThe online version contains supplementary material available at 10.1186/s12864-026-12849-x.", "doi": "10.1186/s12864-026-12849-x", "pmid": "42045837", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13122877"}, {"db": "pii", "key": "10.1186/s12864-026-12849-x"}], "notes": [], "created": "2026-05-11T12:13:32.454Z", "modified": "2026-05-11T12:13:32.461Z"}, {"entity": "publication", "iuid": "89ccc379a277435ca0979bc67c55ad04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89ccc379a277435ca0979bc67c55ad04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89ccc379a277435ca0979bc67c55ad04"}}, "title": "Environmental factors rather than genetics likely drive vitamin D deficiency in idiopathic scoliosis.", "authors": [{"family": "Georgopoulos", "given": "Ioannis", "initials": "I"}, {"family": "Cheng", "given": "Tian", "initials": "T"}, {"family": "Fell", "given": "Daniel", "initials": "D"}, {"family": "Simony", "given": "Ane", "initials": "A"}, {"family": "Andersen", "given": "Mikkel O", "initials": "MO"}, {"family": "Einarsdottir", "given": "El\u00edsabet", "initials": "E"}, {"family": "Karlsson", "given": "Magnus K", "initials": "MK"}, {"family": "Bergstr\u00f6m", "given": "Ingrid", "initials": "I"}, {"family": "Diarbakerli", "given": "Elias", "initials": "E"}, {"family": "Schizas", "given": "Nikos", "initials": "N"}, {"family": "Gerdhem", "given": "Paul", "initials": "P"}], "type": "journal article", "published": "2026-04-23", "journal": {"title": "Spine J", "issn": "1878-1632", "issn-l": "1529-9430"}, "abstract": "Low vitamin D levels in individuals with idiopathic scoliosis (IS) have been reported and suggested as a potential contributor to IS. Bone density has also been shown to be lower in individuals with IS.\n\nTo investigate serum levels of vitamin D, parathyroid hormone (PTH), markers of bone metabolism, and the genetic variation associated with vitamin D levels and bone density in individuals with IS and healthy controls.\n\nCase-control study combining Scandinavian serum cohorts and genetic cohorts.\n\nSerum analyses: 174 individuals with IS and 153 nonscoliotic controls.\n\nA total of 1,394 individuals with IS and 11,108 controls.\n\nSerum 25-hydroxyvitamin D (25OHD), PTH, C-terminal telopeptide (CTX), osteocalcin, calcium, phosphate, creatinine, albumin, alkaline phosphatase, and leptin. Polygenic risk scores (PRS) for 25OHD and bone mineral density (BMD).\n\nSerum samples were analyzed using validated clinical laboratory methods. PRS for 25OHD and BMD were calculated based on previous literature. Statistical analyses were performed using Mann-Whitney U tests, logistic, and linear regression. Mendelian randomization was analyzed using logistic regression and the inverse-variance weighted method.\n\nIn the serum cohort, median 25OHD levels were 54.4 nmol/L in individuals with IS and 67.0 nmol/L in controls. Corresponding PTH levels were 4.0 and 3.2 pmol/L. No statistically significant differences were found in CTX, osteocalcin, alkaline phosphatase, or leptin. PRS for 25OHD was associated with serum 25OHD levels. PRS in individuals with IS and controls were nonsignificant for 25OHD, BMD femoral neck, and BMD lumbar spine. A tendency for lower values for estimated BMD heel was seen in individuals with scoliosis compared to controls.\n\nOur findings indicate altered regulation of the vitamin D-PTH axis in IS, likely driven by environmental rather than genetic factors. Bone turnover markers were comparable between groups; no clear genetically mediated BMD differences could be observed.", "doi": "10.1016/j.spinee.2026.04.026", "pmid": "42034124", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pii", "key": "S1529-9430(26)00132-4"}], "notes": [], "created": "2026-05-27T11:40:51.749Z", "modified": "2026-05-27T11:40:51.753Z"}, {"entity": "publication", "iuid": "01a6b1a78bb54a8f8e4c51b7ca9f3d9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/01a6b1a78bb54a8f8e4c51b7ca9f3d9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/01a6b1a78bb54a8f8e4c51b7ca9f3d9b"}}, "title": "Longitudinal protein profiling of blood during childhood into early adulthood.", "authors": [{"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S", "orcid": "0000-0003-2910-4754", "researcher": {"href": "https://publications.scilifelab.se/researcher/648c9ed3483a4eb8a1d228cf7e59f6a7.json"}}, {"family": "Bj\u00f6rkander", "given": "Sophia", "initials": "S", "orcid": "0000-0002-4600-2883", "researcher": {"href": "https://publications.scilifelab.se/researcher/310af30b841741a790046af03a3cee6d.json"}}, {"family": "Bueno \u00c1lvez", "given": "Mar\u00eda", "initials": "M", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Kebede Merid", "given": "Simon", "initials": "S"}, {"family": "Danielsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6959-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e346ce0d514179baea3c97b615e665.json"}}, {"family": "Bergstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Kull", "given": "Inger", "initials": "I", "orcid": "0000-0001-6096-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f248045358c4711b1d10d7b9fe9649c.json"}}, {"family": "Merritt", "given": "Anne-Sophie", "initials": "AS"}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Klevebro", "given": "Susanna", "initials": "S"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E", "orcid": "0000-0002-8248-0663", "researcher": {"href": "https://publications.scilifelab.se/researcher/3af5a23ba0a847778eea300f745cb143.json"}}], "type": "journal article", "published": "2026-04-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Proteomic research enhances our understanding of health- and disease-related biological processes. Protein profiling during healthy childhood provides important insights into normal physiological development. We longitudinally measured 5416 plasma proteins at four follow-ups during childhood (4-, 8-, 16 years) and early adulthood (24 years) in 100 randomly selected subjects participating in a population-based Swedish cohort, using Olink Explore HT. In total, 3509 proteins were included in the analysis. 54% of the proteins were found to be associated with age, and we observed several protein trajectories from childhood to adulthood based on clustering. In addition to proteins involved in bone, teeth and cartilage formation, we identified differences in proteins involved in neural function, drug metabolism, and hormonal control. There were pronounced sex-related differences in protein levels, particularly at follow-ups 16 and 24, characterized by, for example, growth, response to stimuli and regulation of catabolic processes. We demonstrate dynamic age- and sex-related changes in protein levels during the first two decades of life. Our study results may serve as an important resource in understanding human physiological development, disease etiology, and for future protein biomarker research.", "doi": "10.1038/s41467-026-72095-3", "pmid": "42020385", "labels": {"NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13102979"}, {"db": "pii", "key": "10.1038/s41467-026-72095-3"}], "notes": [], "created": "2026-04-28T06:03:05.109Z", "modified": "2026-04-28T06:03:05.659Z"}, {"entity": "publication", "iuid": "03ccd31f0e5144dc8037a73d69d8ba57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03ccd31f0e5144dc8037a73d69d8ba57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03ccd31f0e5144dc8037a73d69d8ba57"}}, "title": "Genetic and environmental influences on data missingness in developmental cognitive neuroscience.", "authors": [{"family": "Bussu", "given": "G", "initials": "G", "orcid": "0000-0002-6071-3964", "researcher": {"href": "https://publications.scilifelab.se/researcher/c203efb6eec84df2abe07ff811cc9309.json"}}, {"family": "Portugal", "given": "A M", "initials": "AM", "orcid": "0000-0002-3627-0753", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a54163213cc46f88ba1a6d31ac9dc66.json"}}, {"family": "Viktorsson", "given": "C", "initials": "C", "orcid": "0000-0003-2727-2957", "researcher": {"href": "https://publications.scilifelab.se/researcher/465e2969410c4109aaa466735d26002b.json"}}, {"family": "Hardiansyah", "given": "I", "initials": "I"}, {"family": "Falck-Ytter", "given": "T", "initials": "T", "orcid": "0000-0001-9714-0197", "researcher": {"href": "https://publications.scilifelab.se/researcher/ead33894d8054f2291e0be7cbb47e015.json"}}], "type": "journal article", "published": "2026-04-22", "journal": {"title": "Commun Psychol", "issn": "2731-9121", "volume": "4", "issue": "1", "issn-l": null}, "abstract": "Missing data are common in social and clinical sciences and understanding the causes and patterns of missing data is important for selecting analysis approach and for the interpretation of the remaining data. Yet, knowledge about the factors influencing data loss is limited. Here, we assessed the contribution of genes and environments to data missingness across three experiments of infant brain and behavioural development. The sample consisted of 594 infant twins (330 monozygotic, 152 female, 178 male infants; 264 dizygotic, 132 female, 132 male infants) who were assessed with electroencephalography (EEG), pupillometry, and gaze tracking technologies at 5 months of age. Substantial familial factors (additive genetics and/or shared environment) for data missingness were found across all experiments. The amount of missing data showed only a low correlation across the experiments, suggesting a high degree of specificity in the factors contributing to missingness. The results underscore the need to adopt and improve procedural and analytical strategies that minimise data loss and its negative impacts on study conclusions.", "doi": "10.1038/s44271-026-00457-0", "pmid": "42020721", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13102918"}, {"db": "pii", "key": "10.1038/s44271-026-00457-0"}], "notes": [], "created": "2026-06-01T08:45:47.729Z", "modified": "2026-06-01T08:45:47.914Z"}, {"entity": "publication", "iuid": "c115bbb0dfbc4b998a5920a0fb8492e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c115bbb0dfbc4b998a5920a0fb8492e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c115bbb0dfbc4b998a5920a0fb8492e8"}}, "title": "Ancient environmental genome reveals a migratory brown bear individual in Early Holocene Scandinavia.", "authors": [{"family": "Johnson", "given": "Ernst", "initials": "E", "orcid": "0009-0004-0745-2437", "researcher": {"href": "https://publications.scilifelab.se/researcher/891a915ffd054c57b7c0d107c4e1b7e1.json"}}, {"family": "Feinauer", "given": "Isabelle Sofie", "initials": "IS", "orcid": "0009-0004-4615-0810", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d95245a50e408a9643a18b7c0fc3d2.json"}}, {"family": "Regn\u00e9ll", "given": "Carl", "initials": "C", "orcid": "0000-0002-5662-4950", "researcher": {"href": "https://publications.scilifelab.se/researcher/65820ac7ae1c4b6a87dd1334087e677d.json"}}, {"family": "Jin", "given": "Chenyu", "initials": "C", "orcid": "0000-0002-2392-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/165a756337e8489f9621bbaa73fd4f7b.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}, {"family": "Oteo-Garc\u00eda", "given": "Gonzalo", "initials": "G", "orcid": "0000-0002-0957-4014", "researcher": {"href": "https://publications.scilifelab.se/researcher/62bbfad753a943ea94eb9a0384713a17.json"}}, {"family": "Gyllencreutz", "given": "Richard", "initials": "R", "orcid": "0000-0003-3193-8598", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c1d90a4e134dceb7f816725596aa6f.json"}}, {"family": "Greenwood", "given": "Sarah L", "initials": "SL", "orcid": "0000-0003-3048-7916", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b4036ea604943ca9e8d0e2d7ae48d23.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Linderholm", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2026-04-21", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "123", "issue": "16", "pages": "e2527944123", "issn-l": "0027-8424"}, "abstract": "After the last ice age, species migrated into a newly deglaciated Scandinavia. Brown bear recolonization is thought to have occurred from two directions-from the south and the northeast-resulting in a nonoverlapping distribution of two distinct mitochondrial clades. A contact zone in central Sweden separates populations with mitochondrial clade 1a in the south from those with clade 3a in the north. However, a paucity of brown bear subfossils in Scandinavia has limited testing of this prevailing model using ancient DNA. Here, we present a high-coverage brown bear mitogenome (231\u00d7) and nuclear genome-wide data (0.05\u00d7) extracted from lake sediment dated to 9.6 cal. ka BP from northern Sweden, representing the oldest known record of brown bear in the region. At this point in the Early Holocene, the Fennoscandian Ice Sheet was in its final stages of recession. Surprisingly, our analyses suggest that this environmental genome represents one male individual carrying clade 1a and with southern brown bear nuclear ancestry, despite being found far north of the contact zone. This suggests the individual was a migratory bear and had dispersed northward from its birthplace. Our finding adds to the scarce genomic record of Early Holocene brown bears and highlights the use of sedimentary ancient DNA as a powerful source of genomic information.", "doi": "10.1073/pnas.2527944123", "pmid": "41973920", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13099568"}], "notes": [], "created": "2026-05-11T11:39:29.980Z", "modified": "2026-05-11T11:39:30.533Z"}, {"entity": "publication", "iuid": "46c0df4f63584b799ce7923246580642", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46c0df4f63584b799ce7923246580642.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46c0df4f63584b799ce7923246580642"}}, "title": "Unique sex chromosome translocations and evolutionary strata in two Sylvioidea songbird families.", "authors": [{"family": "Brown", "given": "Thomas J", "initials": "TJ", "orcid": "0000-0002-4235-0856", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f23ec5a35d142de898840b16172fdfb.json"}}, {"family": "Ellerstrand", "given": "Simon J", "initials": "SJ", "orcid": "0000-0003-2674-6997", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ed13c7732674cc992f2356848b97a7b.json"}}, {"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Melo", "given": "Martim", "initials": "M", "orcid": "0000-0003-1394-4361", "researcher": {"href": "https://publications.scilifelab.se/researcher/a42199d6eca542c48290db65ae34d940.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2026-04-20", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "27", "issue": "1", "issn-l": "1471-2164"}, "abstract": "Avian genomes are typically stable, yet instances of chromosome fissions, fusions and translocations are known across various lineages. For example, multiple sex chromosome translocations have been described in the superfamily Sylvioidea. In this study, we examine the sex chromosomes in two Sylvioidea families, Nicatoridae and Cisticolidae, using whole-genome data. We found sex-linkage of chromosomes Z and 4A, consistent with findings in other Sylvioidea species. We also identify sex-linkage of parts of chromosome 4, marking a novel discovery for Nicatoridae and a previously documented feature in Cisticolidae. These families are non-sister taxa, and the size of the translocated region of chromosome 4 differs between them, supporting independent translocation events. We uncover variation in recombination suppression and evolutionary strata on chromosome 4 between families, as well as between two genera within Cisticolidae. This study reveals both recurrent and independent trajectories in sex chromosome evolution, deepening our understanding of complex genomes.\n\nThe online version contains supplementary material available at 10.1186/s12864-026-12861-1.", "doi": "10.1186/s12864-026-12861-1", "pmid": "42010480", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13097842"}, {"db": "pii", "key": "10.1186/s12864-026-12861-1"}], "notes": [], "created": "2026-05-27T11:37:59.563Z", "modified": "2026-05-27T11:38:00.060Z"}, {"entity": "publication", "iuid": "87bf60ec792f4e9caf54376f46b3ad5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87bf60ec792f4e9caf54376f46b3ad5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87bf60ec792f4e9caf54376f46b3ad5f"}}, "title": "Rare regulatory mutations disrupt mesenchymal molecular programs driving endocardial cushion formation in bicuspid aortic valve.", "authors": [{"family": "Zhigulev", "given": "Artemy", "initials": "A", "orcid": "0000-0001-9251-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/81a7e8bb937744b5a18ed42d4f2dea5e.json"}}, {"family": "Buyan", "given": "Andrey", "initials": "A", "orcid": "0000-0001-9105-4028", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed79c4583ae342a5ae931e39f7e282a7.json"}}, {"family": "L\u00e1z\u00e1r", "given": "Enik\u0151", "initials": "E", "orcid": "0000-0001-8664-7531", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd94abaf66dd407da5056c04174fc62d.json"}}, {"family": "Gryzunov", "given": "Nikita", "initials": "N", "orcid": "0009-0000-0782-8650", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bb53aa525ff4269936724c077b2d387.json"}}, {"family": "L\u00e5ng", "given": "Karin", "initials": "K"}, {"family": "Mauron", "given": "Rapha\u00ebl", "initials": "R", "orcid": "0009-0004-0909-3554", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa0b2662f1bc40b682ff6923c797877e.json"}}, {"family": "Nozdrin", "given": "Vladimir", "initials": "V", "orcid": "0009-0004-3053-1387", "researcher": {"href": "https://publications.scilifelab.se/researcher/456249fbb9ef48cebc32cc15fe39a35b.json"}}, {"family": "Spalinskas", "given": "Rapolas", "initials": "R", "orcid": "0000-0002-1648-6426", "researcher": {"href": "https://publications.scilifelab.se/researcher/18ca0b7337b849a49861aedf2971067e.json"}}, {"family": "Pradhananga", "given": "Sailendra", "initials": "S"}, {"family": "Petersson Sj\u00f6gren", "given": "Madeleine", "initials": "M"}, {"family": "Schwochow", "given": "Doreen", "initials": "D"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A", "orcid": "0000-0002-3427-9455", "researcher": {"href": "https://publications.scilifelab.se/researcher/9096109f1be94b7197fd249c4193c9d7.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Kulakovskiy", "given": "Ivan V", "initials": "IV", "orcid": "0000-0002-6554-8128", "researcher": {"href": "https://publications.scilifelab.se/researcher/41163cb5ec5d44668f9c6f06edb379ab.json"}}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Bj\u00f6rck", "given": "Hanna M", "initials": "HM", "orcid": "0000-0002-9155-3609", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d162f3de0f941e0a91387357892d656.json"}}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P", "orcid": "0000-0001-6943-9618", "researcher": {"href": "https://publications.scilifelab.se/researcher/d032e807335049b2ac8a5e2398dd48e7.json"}}], "type": "journal article", "published": "2026-04-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Bicuspid aortic valve, a prevalent congenital malformation, predisposes individuals to severe complications. Although the condition exhibits substantial heritability, known protein-coding and common regulatory mutations explain a minority of cases. To assess the contribution of rare regulatory variants, here we integrate high-resolution three-dimensional genome organization profiling with matched whole-genome sequencing from eight individuals with bicuspid aortic valves and eight with standard tricuspid aortic valves. In bicuspid aortic valve patients, mutation-driven chromatin rewiring affected 1.8-fold more valve development genes than in healthy individuals. Genome-wide in silico analyses show that rare regulatory mutations disrupt the transcriptomes of mesenchymal cell populations necessary for endocardial cushion formation. We identify 198 candidate genes associated with bicuspid aortic valve, revealing pronounced heterogeneity and complex interplay between coding and regulatory mutations. Collectively, our findings establish rare regulatory mutations as contributors to the heritability of bicuspid aortic valve and underscore the need to elucidate their mechanistic roles in disease pathogenesis.", "doi": "10.1038/s41467-026-71758-5", "pmid": "41997951", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13090386"}, {"db": "pii", "key": "10.1038/s41467-026-71758-5"}], "notes": [], "created": "2026-05-11T11:41:45.495Z", "modified": "2026-05-11T11:41:46.015Z"}, {"entity": "publication", "iuid": "b32de9be5435484c9597989fb073c05f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b32de9be5435484c9597989fb073c05f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b32de9be5435484c9597989fb073c05f"}}, "title": "RUVBL1 and RUVBL2 are druggable MYC effector regulators in neuroblastoma cells.", "authors": [{"family": "Siaw", "given": "Joachim Tetteh", "initials": "JT"}, {"family": "Claeys", "given": "Arne", "initials": "A"}, {"family": "Lai", "given": "Wei-Yun", "initials": "WY"}, {"family": "Boren\u00e4s", "given": "Marcus", "initials": "M"}, {"family": "Hilgert", "given": "Elien", "initials": "E"}, {"family": "Bekaert", "given": "Sarah-Lee", "initials": "SL"}, {"family": "Sanders", "given": "Ellen", "initials": "E"}, {"family": "Kaya", "given": "Irem", "initials": "I"}, {"family": "Van Dorpe", "given": "Jo", "initials": "J"}, {"family": "Speleman", "given": "Frank", "initials": "F"}, {"family": "Durinck", "given": "Kaat", "initials": "K"}, {"family": "Hallberg", "given": "Bengt", "initials": "B"}, {"family": "Palmer", "given": "Ruth H", "initials": "RH"}, {"family": "Van den Eynden", "given": "Jimmy", "initials": "J"}], "type": "journal article", "published": "2026-04-17", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "29", "issue": "4", "pages": "115236", "issn-l": "2589-0042"}, "abstract": "High-risk neuroblastoma is characterized by MYCN amplification and high MYCN or MYC gene expression. These patients have a poor prognosis and there is an urgent need for more effective drugs. While strategies to develop inhibitors that directly target the MYC proteins have remained largely unsuccessful, recent preclinical studies have identified ATR, a key protein of the DNA damage response, as a promising alternative therapeutic target. Here, we identified a strong RUVBL1 and RUVBL2 signature in transcriptomics data derived from different MYCN-driven mice tumors treated with ATR inhibitors. The RUVBL proteins form a complex with ATPase activity that has broad cellular functions and we demonstrate that pharmacological inhibition of this protein complex results in a strong reduction of MYC(N) signaling, cell-cycle arrest, DNA damage, and apoptosis. We confirmed the association with MYCN and identified the RUVBL genes as independent prognostic biomarkers in human primary neuroblastoma data.", "doi": "10.1016/j.isci.2026.115236", "pmid": "41940329", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13049659"}, {"db": "pii", "key": "S2589-0042(26)00611-5"}], "notes": [], "created": "2026-04-10T13:11:20.241Z", "modified": "2026-04-10T13:11:20.252Z"}, {"entity": "publication", "iuid": "80874800e5764f2299c86ac54a90127a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80874800e5764f2299c86ac54a90127a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80874800e5764f2299c86ac54a90127a"}}, "title": "Genomic insights into fragmentation and translocation in European green toads.", "authors": [{"family": "Walderich", "given": "Leonie Muriel", "initials": "LM"}, {"family": "Susanto", "given": "Alvin Wiwiet", "initials": "AW"}, {"family": "Svensson", "given": "Mikael", "initials": "M"}, {"family": "Fohrman", "given": "Anna", "initials": "A"}, {"family": "Wir\u00e9n", "given": "Mats", "initials": "M"}, {"family": "O'Dwyer", "given": "Rachael", "initials": "R"}, {"family": "F\u00f6rs\u00e4ter", "given": "Kristofer", "initials": "K"}, {"family": "R\u00f6din-M\u00f6rch", "given": "Patrik", "initials": "P"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2026-04-17", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "29", "issue": "4", "pages": "115395", "issn-l": "2589-0042"}, "abstract": "The European green toad (Bufotes viridis) is Sweden's most threatened amphibian. Its range has contracted over the past century, with many local extinctions; remaining populations are fragmented and often isolated. Since the 1990s, conservation has focused on translocations to existing breeding sites and new localities, but many efforts have had limited success. We detected lower genetic diversity in Scandinavian populations (southern Sweden and nearby Denmark) than in Poland, plus strong structure and differentiation among Scandinavian subpopulations, implying unexpectedly low gene flow despite translocations. Small, isolated populations are strongly affected by drift, and whole-genome analyses reveal inbreeding and high genetic load in some subpopulations. We recommend reassessing source populations for translocations: the stock used in captive breeding and most past releases shows intermediate diversity but also signs of divergent selection and putative local adaptation. Management should balance minimizing inbreeding depression against risks of outbreeding depression and erosion of local adaptation risks.", "doi": "10.1016/j.isci.2026.115395", "pmid": "42006334", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13084336"}, {"db": "pii", "key": "S2589-0042(26)00770-4"}], "notes": [], "created": "2026-05-11T13:10:40.099Z", "modified": "2026-05-11T13:10:40.109Z"}, {"entity": "publication", "iuid": "c45c714869d64a00996f49c14d6bedab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c45c714869d64a00996f49c14d6bedab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c45c714869d64a00996f49c14d6bedab"}}, "title": "Minor hemolysin-coregulated proteins (Hcp) form heteromeric complexes and mediate effector secretion in Bacteroidales type VI secretion systems.", "authors": [{"family": "San-Miguel", "given": "Sergio G", "initials": "SG"}, {"family": "Hillier", "given": "Jessica B", "initials": "JB"}, {"family": "Saleh Al-Ammari", "given": "Manal Kamal", "initials": "MK"}, {"family": "Johansson", "given": "Emma", "initials": "E"}, {"family": "Kowalska", "given": "Anna", "initials": "A"}, {"family": "Sauer", "given": "Uwe", "initials": "U", "orcid": "0000-0002-3420-439X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d011e944ae54d47aed374d548007812.json"}}, {"family": "Batista", "given": "Paulo Ricardo", "initials": "PR"}, {"family": "Sandblad", "given": "Linda", "initials": "L", "orcid": "0000-0003-3492-3287", "researcher": {"href": "https://publications.scilifelab.se/researcher/070825e0190a4e9a932e79663d2bc89f.json"}}, {"family": "Uhlin", "given": "Bernt Eric", "initials": "BE", "orcid": "0000-0002-2991-8072", "researcher": {"href": "https://publications.scilifelab.se/researcher/9faa19d33fd84728bb6df987ba16475f.json"}}, {"family": "Cisneros", "given": "David A", "initials": "DA", "orcid": "0000-0001-9919-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/19f7a4aba7af436899b5d63f95f0dcda.json"}}], "type": "journal article", "published": "2026-04-16", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "pages": "111464", "issn-l": "0021-9258"}, "abstract": "The type VI secretion system (T6SS) is a protein complex found in Gram-negative bacteria that mediates intercellular antagonism. Hemolysin-coregulated proteins (Hcp) are major structural proteins in these systems. Hcp forms hexameric rings that stack to create an inner tube structure essential for translocating effector proteins into target cells. In gut Bacteroidales, T6SS loci encode multiple Hcp proteins with unknown function. The gut commensal Bacteroides fragilis encodes five Hcp subunits (sHcp and Hcp1-4) that have low sequence similarity. In this study, we investigated the roles of these proteins. Interaction studies showed that sHcp forms homohexamers, which is consistent with a major role of forming the bulk of the inner tube. In contrast, the less abundant minor Hcp1-4 were shown to form an interaction network involving heteromeric complexes. Biochemical and genetic analyses demonstrated that Hcp1 and Hcp2 assemble into heterohexamers and that this complex recognizes the secreted effector Bte1, contributing to its secretion. Finally, we showed that Hcp modules, which are encoded in highly syntenic regions in T6SS loci of Bacteroidales, cluster with effectors. These results imply that the minor Hcps genetically cosegregate with cognate effectors, contributing to effector cassette variability. Thus, minor Hcp subunits function as recognition particles for effectors to mediate secretion, which appears to be a conserved trait in Bacteroidales T6SSs. Exploiting these features could facilitate the characterization of unknown effectors by copurifying them with their cognate Hcps. This approach may reveal new insights into bacterial interactions and the mechanisms that establish gut biodiversity.", "doi": "10.1016/j.jbc.2026.111464", "pmid": "41999889", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9258(26)00336-4"}], "notes": [], "created": "2026-04-24T08:57:10.339Z", "modified": "2026-05-04T07:55:01.391Z"}, {"entity": "publication", "iuid": "239c56876b514de5ac01c6d5c716ba98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/239c56876b514de5ac01c6d5c716ba98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/239c56876b514de5ac01c6d5c716ba98"}}, "title": "Dabigatran Concentrations in an Actively Breastfeeding Mother-Infant Dyad: Extending the Evidence for Oral Thromboprophylaxis Postpartum.", "authors": [{"family": "Green", "given": "Rasmus W", "initials": "RW", "orcid": "0000-0001-6575-2447", "researcher": {"href": "https://publications.scilifelab.se/researcher/35553a3c60d842a4a31d650a5b793e17.json"}}, {"family": "Saleh", "given": "Aljona", "initials": "A", "orcid": "0009-0002-2121-043X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c469c0a07dc746c2a16b122c2269480c.json"}}, {"family": "Baranczewski", "given": "Pawel", "initials": "P", "orcid": "0000-0001-5772-6791", "researcher": {"href": "https://publications.scilifelab.se/researcher/47f7af2466c14275a42aad4a431b2dcb.json"}}], "type": "letter", "published": "2026-04-16", "journal": {"title": "Am. J. Hematol.", "issn": "1096-8652", "issn-l": "0361-8609"}, "abstract": null, "doi": "10.1002/ajh.70318", "pmid": "41992716", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-05-14T20:17:57.798Z", "modified": "2026-05-14T20:17:58.184Z"}, {"entity": "publication", "iuid": "c67e37951ff244288a56301faa275a0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c67e37951ff244288a56301faa275a0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c67e37951ff244288a56301faa275a0d"}}, "title": "Evidence for cable bacteria inhabiting deep in anoxic sediment reveals a novel ecological niche.", "authors": [{"family": "Fonseca", "given": "Alexis", "initials": "A"}, {"family": "Hermans", "given": "Martijn", "initials": "M"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}, {"family": "Stranne", "given": "Christian", "initials": "C"}, {"family": "Norkko", "given": "Alf", "initials": "A"}, {"family": "Gustafsson", "given": "Bo G", "initials": "BG"}, {"family": "Humborg", "given": "Christoph", "initials": "C"}], "type": "journal article", "published": "2026-04-15", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "21", "issue": "1", "issn-l": null}, "abstract": "Cable bacteria are filamentous sulphide-oxidisers capable of cm-scale electron transport. They are generally considered restricted to the upper few oxic-suboxic cm of marine sediments, where they couple sulphide oxidation to oxygen or nitrate reduction. Despite their influence on redox gradients, trace metal mobility, and nutrient cycling, their presence and activity in deeper anoxic sediment layers remain unknown. The presence and activity of marine cable bacteria (Candidatus Electrothrix) were investigated at four stations in Sweden and Finland, including deep vertical profiles of anoxic sediment layers, to assess their presence and activity under different environmental contexts.\n\nUsing metatranscriptomic data for rRNA-based community profiling and gene expression combined with porewater geochemistry, evidence of abundant and active cable bacteria was found, peaking below 20 cm depth in deep anoxic sediment layers of Kolj\u00f6 Fjord on the Swedish West Coast. This zone coincided with elevated gene expressions related to sulphide oxidation (including sqr) and nitrate reduction (napA), as well as an abundant presence of sulphide and a sharp nitrate peak. Phylogenetic analyses revealed a diverse assemblage of Ca. Electrothrix includes several potential novel taxa. The co-occurrence of cable bacteria activity, sulphide availability, and a nitrate peak at depth suggests that these organisms may be supported by local nitrate production under anoxic conditions.\n\nOur findings challenge the prevailing view that cable bacteria are restricted to shallow sediment horizons and demonstrate their activity and diversity in deep, anoxic layers. This expands the known ecological niche of cable bacteria and suggests that locally produced nitrate under anoxic conditions may facilitate their activity at depth. This discovery advances our understanding of ecology in anoxic marine environments, providing new insights into marine cable bacteria, sediment biogeochemistry, and analogues of early Earth microbial ecosystems.", "doi": "10.1186/s40793-026-00895-7", "pmid": "41987322", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13081432"}, {"db": "pii", "key": "10.1186/s40793-026-00895-7"}], "notes": [], "created": "2026-05-11T11:49:40.138Z", "modified": "2026-05-11T11:49:40.148Z"}, {"entity": "publication", "iuid": "0e45658433fb4fd68d5f344433957d24", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e45658433fb4fd68d5f344433957d24.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e45658433fb4fd68d5f344433957d24"}}, "title": "A transcriptional atlas of the pubertal human growth plate reveals two populations of stem cells and direct effect of growth hormone.", "authors": [{"family": "Chu", "given": "Nelson Tsz Long", "initials": "NTL", "orcid": "0000-0001-8553-6880", "researcher": {"href": "https://publications.scilifelab.se/researcher/771e0a6c700f4b4f9765f9a2811608eb.json"}}, {"family": "Dregval", "given": "Ostap", "initials": "O", "orcid": "0000-0002-9939-6492", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a3d8ecff20444e9bf82f702e21e736c.json"}}, {"family": "Zaman", "given": "Farasat", "initials": "F", "orcid": "0000-0002-1832-1051", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c082df96e5c43afbca28c5c6f8e7810.json"}}, {"family": "Li", "given": "Lei", "initials": "L", "orcid": "0000-0002-8026-3665", "researcher": {"href": "https://publications.scilifelab.se/researcher/31e881d87f094a92bc6b34f734ffe12f.json"}}, {"family": "Tian", "given": "Xin", "initials": "X"}, {"family": "Liu", "given": "Xin", "initials": "X"}, {"family": "Trompet", "given": "Dana", "initials": "D", "orcid": "0000-0001-9472-6184", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ef4d02ec2e1427088522df2a759bf3a.json"}}, {"family": "Zhou", "given": "Baoyi", "initials": "B"}, {"family": "Heinonen", "given": "Jussi O", "initials": "JO"}, {"family": "Ohlsson", "given": "Claes", "initials": "C", "orcid": "0000-0002-9633-2805", "researcher": {"href": "https://publications.scilifelab.se/researcher/995dac358caa4a169fc889b7a3eef44a.json"}}, {"family": "S\u00e4vendahl", "given": "Lars", "initials": "L", "orcid": "0000-0003-1067-4976", "researcher": {"href": "https://publications.scilifelab.se/researcher/6da067b5b4a34625806e9335fa921f09.json"}}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}, {"family": "Chagin", "given": "Andrei S", "initials": "AS", "orcid": "0000-0002-2696-5850", "researcher": {"href": "https://publications.scilifelab.se/researcher/909bca2fc68645e980a93b99dc150e4c.json"}}], "type": "journal article", "published": "2026-04-15", "journal": {"title": "Sci Transl Med", "issn": "1946-6242", "volume": "18", "issue": "845", "pages": "eadw3590", "issn-l": "1946-6234"}, "abstract": "The cartilaginous growth plate is a critical organ responsible for longitudinal bone growth. It closes after puberty in humans but remains open throughout life in mice. Although cartilage stem cells have been identified in murine growth plates, their existence in humans and their regulation by growth hormone (GH), the most widely used therapy for growth retardation, remain unknown. Here, we characterized the cellular and molecular organization of early pubertal human growth plates using unique surgical specimens from growth-restricting procedures and examined their direct responsiveness to GH. Single-cell and spatial analyses revealed two distinct stemlike populations in the resting zone, differing in proliferative activity, molecular identity, and regulatory cues. The root stem cells express multiple skeletal stem cell markers but not parathyroid hormone-related peptide and reside in a specialized microenvironment low in WNT and TGF-\u03b2 growth factors. A similar population was identified in transcriptionally profiled unsorted murine growth plates, and clonal lineage tracing demonstrated that these root cells, marked by expression of the Prrx1 gene, generate extensive chondrocyte clones and differentiate into stromal and osteoblastic lineages, confirming their stem cell properties. Human growth plate explant cultures showed that GH directly activates JAK/STAT, TGF-\u03b2, and ERK intracellular signaling pathways, inhibits AKT signaling, and stimulates cartilage growth and proliferation of cartilage stem cells and chondrocytes in the proliferative zone. Together, these findings uncover a conserved dual stem cell organization in human and mouse growth plates and define direct mechanisms of GH action, providing a framework for optimizing growth-promoting therapies.", "doi": "10.1126/scitranslmed.adw3590", "pmid": "41984930", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-05-11T12:02:43.939Z", "modified": "2026-05-11T12:02:44.448Z"}, {"entity": "publication", "iuid": "510c69c23c874b20bf9361bd6a5f1796", "links": {"self": {"href": "https://publications.scilifelab.se/publication/510c69c23c874b20bf9361bd6a5f1796.json"}, "display": {"href": "https://publications.scilifelab.se/publication/510c69c23c874b20bf9361bd6a5f1796"}}, "title": "A tumor-associated photoreceptor signature unifies distinct central nervous system malignancies.", "authors": [{"family": "Gudenas", "given": "Brian L", "initials": "BL"}, {"family": "Ahmad", "given": "Shiekh Tanveer", "initials": "ST"}, {"family": "Englinger", "given": "Bernhard", "initials": "B"}, {"family": "Liu", "given": "Anthony P Y", "initials": "APY"}, {"family": "Zhao", "given": "Miao", "initials": "M"}, {"family": "Paul", "given": "Leena", "initials": "L"}, {"family": "Hadley", "given": "Jennifer", "initials": "J"}, {"family": "Li", "given": "Yiran", "initials": "Y"}, {"family": "Batts", "given": "Melissa", "initials": "M"}, {"family": "Mittal", "given": "Priya", "initials": "P"}, {"family": "Wu", "given": "Stephanie C", "initials": "SC"}, {"family": "Lewis", "given": "Sara A", "initials": "SA"}, {"family": "Han", "given": "Katie", "initials": "K"}, {"family": "Soliman", "given": "Taha", "initials": "T"}, {"family": "Lin", "given": "Hong", "initials": "H"}, {"family": "Janke", "given": "Laure", "initials": "L"}, {"family": "Meredith", "given": "David", "initials": "D"}, {"family": "Pfaff", "given": "Elke", "initials": "E"}, {"family": "Gojo", "given": "Johannes", "initials": "J"}, {"family": "Cotter", "given": "Jennifer", "initials": "J"}, {"family": "Klimo", "given": "Paul", "initials": "P"}, {"family": "Boop", "given": "Frederick A", "initials": "FA"}, {"family": "Gajjar", "given": "Amar", "initials": "A"}, {"family": "Robinson", "given": "Giles W", "initials": "GW"}, {"family": "Ros\u00e9n", "given": "Gabriela", "initials": "G"}, {"family": "Alexandrescu", "given": "Sanda", "initials": "S"}, {"family": "Jones", "given": "David T W", "initials": "DTW"}, {"family": "Orr", "given": "Brent A", "initials": "BA"}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ"}, {"family": "Filbin", "given": "Mariella G", "initials": "MG"}, {"family": "Northcott", "given": "Paul A", "initials": "PA"}], "type": "journal article", "published": "2026-04-13", "journal": {"title": "Cancer Cell", "issn": "1878-3686", "volume": "44", "issue": "4", "pages": "831-845.e10", "issn-l": "1535-6108"}, "abstract": "Pineoblastoma is a clinically aggressive childhood brain tumor composed of distinct molecular subgroups with divergent driver genes, demographics, and clinical outcomes. To identify developmental origins and mechanisms governing disease pathogenesis, we derive single-cell transcriptomes from pineal parenchymal tumors, aligning malignant cells with developmental counterparts to retrace cellular origins. Integrative computational analyses map pineoblastoma origins to transient, cycling pinealocyte progenitors during development. Lineage-specific perturbation of suspected drivers in the early pineal gland yields preclinical models representative of consensus molecular subgroups. Multi-omic characterization of patient tumors and these models uncover a tumor-associated photoreceptor signature (TAPS) common to pineoblastoma, retinoblastoma, and Group 3 medulloblastoma. Transcriptional activity of this signature within respective cellular origins establishes a developmental basis for molecular similarities between entities. Photoreceptor signature constituents are selective dependencies across these anatomically distinct central nervous system malignancies, motivating future studies evaluating developmentally encoded programs of malignancy as potential therapeutic liabilities.", "doi": "10.1016/j.ccell.2026.02.010", "pmid": "41791379", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2149981"}, {"db": "pmc", "key": "PMC13123407"}, {"db": "pii", "key": "S1535-6108(26)00108-X"}], "notes": [], "created": "2026-06-01T11:10:55.839Z", "modified": "2026-06-01T11:10:55.858Z"}, {"entity": "publication", "iuid": "302ea24f73a84f0e8853a9e9b53eb13f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/302ea24f73a84f0e8853a9e9b53eb13f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/302ea24f73a84f0e8853a9e9b53eb13f"}}, "title": "Dimethyl Fumarate, But Not Rituximab, Reduces Serum GFAP Levels and PIRMA in Relapsing\u2013Remitting MS", "authors": [{"family": "Shawket", "given": "F", "initials": "F"}, {"family": "Lycke", "given": "J", "initials": "J"}, {"family": "Salzer", "given": "J", "initials": "J"}, {"family": "Piehl", "given": "F", "initials": "F", "orcid": "0000-0001-8329-5219", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee04062fbee34836a4fa3f4d2e8076cd.json"}}, {"family": "Fink", "given": "K", "initials": "K"}, {"family": "Lange", "given": "N", "initials": "N"}, {"family": "Mellerg\u00e5rd", "given": "J", "initials": "J", "orcid": "0000-0003-0120-3734", "researcher": {"href": "https://publications.scilifelab.se/researcher/f471bdcfc7fc4c2fb282484ac7e148bd.json"}}, {"family": "Malmestr\u00f6m", "given": "C", "initials": "C"}, {"family": "Sundstr\u00f6m", "given": "P", "initials": "P"}, {"family": "Erngren", "given": "I", "initials": "I", "orcid": "0000-0001-7867-9525", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8a16aaaf5194acba6b8649690a101d8.json"}}, {"family": "al\u2010Grety", "given": "A", "initials": "A"}, {"family": "Freyhult", "given": "E", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Kultima", "given": "K", "initials": "K", "orcid": "0000-0002-0680-1410", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ae376585168459681f5e2cae0c75b96.json"}}, {"family": "Burman", "given": "J", "initials": "J"}, {"family": "Svenningsson", "given": "A", "initials": "A", "orcid": "0000-0003-0663-2220", "researcher": {"href": "https://publications.scilifelab.se/researcher/73156fb41b544d82ad4c022d2ca12fc3.json"}}], "type": "journal-article", "published": "2026-04-12", "journal": {"title": "Ann Clin Transl Neurol", "issn": "2328-9503", "issn-l": "2328-9503"}, "abstract": "Serum neurofilament light chain (sNfL) and glial fibrillary acidic protein (sGFAP) levels are believed to reflect mainly acute and chronic disease processes in multiple sclerosis (MS), respectively. In this study, we investigated whether dimethyl fumarate (DMF) and rituximab (RTX) differentially affect these biomarkers.\n\nRIFUND-MS was a 2-year, rater-blinded, 1:1 randomized controlled multicenter trial comparing DMF and RTX in relapsing-remitting multiple sclerosis (RRMS). Serum samples for analysis of sNFL and sGFAP were collected at baseline and 0, 6, 12 and 24. Log-transformed biomarker data were analyzed with linear mixed models, based on intention to treat (ITT), per protocol (PP) and accounting for therapy switches. Cox proportional hazards models were performed to evaluate progression outcomes.\n\nOf 200 participants, 197 were analyzed. Based on ITT, sNfL decreased significantly in both arms from baseline to month 24; by 50.7% (CI 43.7%-56.8%; p < 0.001) with RTX, and by 46.4% (CI 38.6%-53.2%; p < 0.001) with DMF, no differences between treatments (global p-value: ITT = 0.06; PP = 0.08; switch group = 0.15). In contrast, sGFAP remained stable in RTX (3.6% decrease; CI -7.8%-13.8%, p = 0.81) but decreased with DMF (18.4%; CI 8.5%-27.2%; p < 0.001). Global analyses favored DMF (ITT = 0.02; PP = 0.004; switch group = 0.74). The risk of progression independent of relapse and MRI activity (PIRMA) was higher with RTX (HR 3.3, CI 1.1-10, p = 0.04).\n\nBoth RTX and DMF reduced sNfL levels, consistent with suppression of acute inflammatory disease activity. However, only DMF was associated with a sustained reduction in sGFAP and a lower risk of non-inflammatory disability progression. These findings suggest that DMF may exert additional effects on astrocyte-related or compartmentalized CNS pathology beyond peripheral immune modulation.", "doi": "10.1002/acn3.70395", "pmid": "41968564", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-04-14T06:47:42.291Z", "modified": "2026-04-16T09:41:54.416Z"}, {"entity": "publication", "iuid": "11b37392972444f5998ff8f14ca156cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11b37392972444f5998ff8f14ca156cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11b37392972444f5998ff8f14ca156cd"}}, "title": "An integrative molecular map of pediatric B-cell precursor acute lymphoblastic leukemia.", "authors": [{"family": "Krali", "given": "Olga", "initials": "O", "orcid": "0000-0002-6436-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a6e2f99d3b4758a10af78b93777779.json"}}, {"family": "Enblad", "given": "Anna Pia", "initials": "AP"}, {"family": "Sulyaeva", "given": "Julia", "initials": "J"}, {"family": "Gogishvili", "given": "Dea", "initials": "D"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Harila", "given": "Arja", "initials": "A"}, {"family": "Andersson", "given": "Claes", "initials": "C"}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M", "orcid": "0000-0001-6190-3439", "researcher": {"href": "https://publications.scilifelab.se/researcher/be7efa5a7c9a4da18b397a07ebd8d9ec.json"}}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2026-04-11", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "6", "issue": "1", "issn-l": null}, "abstract": "The molecular landscape of pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) has been extensively characterized through single-modality studies. However, the interplay between molecular modalities and their collective influence on treatment response and outcomes remains poorly understood.\n\nWe integrated genomic, epigenomic, transcriptomic, and ex vivo drug response data from 1231 patients diagnosed with BCP-ALL. Using Multi-Omics Factor Analysis, we identified signatures explaining key aspects of the integrative molecular landscape, referred to as cross-modal elements (CMEs). The CME-derived signatures were introduced into pathway and intermodal network analyses, while their impact on patient outcomes was assessed through survival modeling.\n\nPathway and network analyses annotate the resulting integrative CMEs, linking them to key biological processes, including disease development, cellular regulatory processes, metabolic pathways, and drug response. By leveraging correlations between DNA methylation and ex vivo response to doxorubicin, we stratify patients with hyperdiploidy into subgroups that differ in relapse-free survival. These signatures are independent of clinical variables. Survival models incorporating CME-selected ex-vivo drug responses combined with clinical data improve risk prediction compared to clinical models alone (FDR < 0.05), demonstrating the potential of integrative multiomics in refining risk stratification.\n\nOur study highlights the importance of multimodal data integration in BCP-ALL to provide biological insights with potential relevance for precision medicine.", "doi": "10.1038/s43856-026-01568-9", "pmid": "41965886", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13079846"}, {"db": "pii", "key": "10.1038/s43856-026-01568-9"}], "notes": [], "created": "2026-06-01T11:13:50.747Z", "modified": "2026-06-01T11:13:50.765Z"}, {"entity": "publication", "iuid": "22d1c899e817411c810114fd519eebb3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/22d1c899e817411c810114fd519eebb3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/22d1c899e817411c810114fd519eebb3"}}, "title": "A Phytophthora infestans CRN1-derived small RNA is predicted to target the potato immune regulator EDS1.", "authors": [{"family": "Singh", "given": "Shailja", "initials": "S"}, {"family": "Hu", "given": "Xinyi", "initials": "X"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2026-04-10", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "17", "pages": "1791978", "issn-l": "1664-462X"}, "abstract": "The late blight pathogen, Phytophthora infestans (Pi), causes severe damage to plants in the Solanaceae family. Although knowledge regarding the P. infestans-mediated manipulation of critical components in the plant defense system is growing, many questions remain unanswered. Herein, we aimed to examine the role of Argonaute 1 (AGO1) associated small RNAs in this interaction. Of particular interest was the early communication between the host and the pathogen. To visualize the cellular dynamics underlying potential cross-kingdom RNA trafficking, we first examined the localization and accumulation patterns of plant extracellular vesicles (EVs) and multivesicular bodies (MVBs) using a handful of markers. MVBs were present not only at the plant plasma membrane but also in the germ tube of the invading pathogen. The enrichment of MVBs decreased as the infection process proceeded. At 3.0 days post-inoculation, co-localization between AGO1 from P. infestans and StARA6 was not seen even at the swollen tip of the germ tube. Three Crinkler effector genes encoding small RNAs were found after coimmunoprecipitation, sequencing and extensive bioinformatic analysis. PiCRN1 caused more severe disease compared with PiCRN3, which carries a typical Crinkler (CRN) LFLAK domain. This difference may result from activation of a CRN1-derived siRNA predicted to target the enhanced disease susceptibility 1 (EDS1) gene in potato. To examine whether the observed phenotypic effects can be attributed to any EV cargo from the potato host, we set up a procedure to isolate EVs from P. infestans-infected potato leaves. However, the tiny EV yield obtained during the early infection phase prevented us from such analysis. The understanding of effector cell trafficking and small RNA reprogramming of host plant genes remain elusive in this pathosystem.", "doi": "10.3389/fpls.2026.1791978", "pmid": "42040283", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13106546"}], "notes": [], "created": "2026-05-11T12:26:39.885Z", "modified": "2026-05-11T12:26:39.900Z"}, {"entity": "publication", "iuid": "1e2a6a80e6314c9e9c235060aee84268", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e2a6a80e6314c9e9c235060aee84268.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e2a6a80e6314c9e9c235060aee84268"}}, "title": "TNF\u03b1 signaling in radiation-induced chronic bowel dysfunction suggests therapeutic potential for IBD biologics", "authors": [{"family": "Devarakonda", "given": "Sravani", "initials": "S"}, {"family": "Patel", "given": "Piyush", "initials": "P"}, {"family": "Toft Mor\u00e9n", "given": "Amelie", "initials": "A"}, {"family": "Bergmark", "given": "Karin", "initials": "K"}, {"family": "Bamfarahnak", "given": "Mohammad", "initials": "M"}, {"family": "Buske", "given": "Patrik A", "initials": "PA"}, {"family": "Peng", "given": "Yueling", "initials": "Y"}, {"family": "Thorsell", "given": "Annika", "initials": "A"}, {"family": "Li", "given": "Yuan", "initials": "Y"}, {"family": "Fagman", "given": "Henrik", "initials": "H"}, {"family": "Fransson", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-4762-901X", "researcher": {"href": "https://publications.scilifelab.se/researcher/30428cafc89647768f6c69eecf98efcf.json"}}, {"family": "Heden", "given": "Lisen", "initials": "L"}, {"family": "Gustafsson", "given": "Karin", "initials": "K"}, {"family": "Zhu", "given": "Changlian", "initials": "C"}, {"family": "Hedenstr\u00f6m", "given": "Per", "initials": "P"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c6a2dde2d8f40ef82dfba0cf1b52c0d.json"}}, {"family": "Bull", "given": "Cecilia", "initials": "C"}], "type": "journal-article", "published": "2026-04-09", "journal": {"title": "Mol. Med.", "issn": "1528-3658", "volume": "32", "issue": "1", "issn-l": "1076-1551"}, "abstract": null, "doi": "10.1186/s10020-026-01441-4", "pmid": "41957709", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-04-10T07:07:13.665Z", "modified": "2026-04-16T09:42:11.163Z"}, {"entity": "publication", "iuid": "e68983c84bbc41d8a88758e197b58a33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e68983c84bbc41d8a88758e197b58a33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e68983c84bbc41d8a88758e197b58a33"}}, "title": "Potent Neuronal Nicotinamide Adenine Dinucleotide-Boosting Tetrahydroquinoxalines: Structure-Activity Relationships and Early Drug Metabolism and Pharmacokinetics Evaluation.", "authors": [{"family": "Cu\u0159\u00ednov\u00e1", "given": "Petra", "initials": "P", "orcid": "0000-0001-8264-7032", "researcher": {"href": "https://publications.scilifelab.se/researcher/f196559d7e954e448879878768bc213e.json"}}, {"family": "J\u00f6e", "given": "Melissa", "initials": "M"}, {"family": "Cesar", "given": "Filip", "initials": "F"}, {"family": "Nicol", "given": "Alan", "initials": "A"}, {"family": "Schwan", "given": "Kristi\u00e1n", "initials": "K"}, {"family": "Kohout", "given": "Michal", "initials": "M", "orcid": "0000-0003-1447-4453", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4f2547f153b43d79c0364607cd518c6.json"}}, {"family": "Varrichio", "given": "Carmine", "initials": "C"}, {"family": "Saleh", "given": "Aljona", "initials": "A"}, {"family": "Wheelock", "given": "Craig E", "initials": "CE", "orcid": "0000-0002-8113-0653", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3cd2b99e3e9486ba41030c809a48c51.json"}}, {"family": "J\u00f3hannesson", "given": "Gauti", "initials": "G"}, {"family": "Eigner", "given": "V\u00e1clav", "initials": "V"}, {"family": "Tribble", "given": "James R", "initials": "JR"}, {"family": "Brancale", "given": "Andrea", "initials": "A", "orcid": "0000-0002-9728-3419", "researcher": {"href": "https://publications.scilifelab.se/researcher/7aa54df57e794ee3a2b98108bd694277.json"}}, {"family": "Williams", "given": "Pete A", "initials": "PA", "orcid": "0000-0001-6194-8397", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b4d7eb42dcd4c489a97198a043b3806.json"}}], "type": "journal article", "published": "2026-04-09", "journal": {"title": "ACS Med Chem Lett", "issn": "1948-5875", "volume": "17", "issue": "4", "pages": "916-924", "issn-l": "1948-5875"}, "abstract": "We designed and synthesized a series of novel 1,2,3,4-tetrahydroquinoxaline derivatives and evaluated their ability to increase nicotinamide adenine dinucleotide (NAD) levels in primary cortical neurons. Several compounds demonstrated nanomolar potency and enabled the establishment of clear structure-activity relationships (SAR), highlighting key substituents required for activity. Qualitative 3DSAR analysis further identified favorable steric, electrostatic, and hydrophobic features associated with NAD enhancement. Selected lead compounds were assessed for in vitro drug metabolism and pharmacokinetics (DMPK) properties, showing good cell permeability and species-dependent metabolic stability in liver microsomes, with improved stability in human systems compared with rodent systems. These findings identify tetrahydroquinoxalines as a promising class of neuronal NAD-boosting agents and provide a strong foundation for further optimization toward neuroprotective drug candidates.", "doi": "10.1021/acsmedchemlett.6c00058", "pmid": "41982735", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13071616"}], "notes": [], "created": "2026-05-14T20:21:50.854Z", "modified": "2026-05-14T20:21:51.275Z"}, {"entity": "publication", "iuid": "8be8d00d65424632a6066715fa2207b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8be8d00d65424632a6066715fa2207b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8be8d00d65424632a6066715fa2207b8"}}, "title": "Lectin pathway of complement in SLE: MAP-1 as a marker of haematological manifestations and elevated type I interferon activity.", "authors": [{"family": "Lindel\u00f6f", "given": "Linnea", "initials": "L", "orcid": "0000-0002-3654-8874", "researcher": {"href": "https://publications.scilifelab.se/researcher/65f6c8233c5547f2885b3e55bbec2601.json"}}, {"family": "Garred", "given": "Peter", "initials": "P"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Wahl V\u00e6lum", "given": "Sasha", "initials": "S", "orcid": "0009-0006-1378-9591", "researcher": {"href": "https://publications.scilifelab.se/researcher/6668483bc5d1464f839e525848a5b84c.json"}}, {"family": "Holten Petersen", "given": "Lotte", "initials": "L"}, {"family": "Leonard", "given": "Dag", "initials": "D", "orcid": "0000-0002-6275-7282", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ed25c2f495484db4757f4fef51abae.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Oke", "given": "Vilija", "initials": "V", "orcid": "0000-0002-1834-2688", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5115e955050467694c2e2396706066a.json"}}, {"family": "Niewold", "given": "Timothy B", "initials": "TB", "orcid": "0000-0003-3532-6660", "researcher": {"href": "https://publications.scilifelab.se/researcher/89b178dc1ef34fa4b4ef34e71b9ac1e5.json"}}, {"family": "Diaz-Gallo", "given": "Lina-Marcela", "initials": "LM", "orcid": "0000-0002-5688-0102", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fc169ccfb154ef29c62f78044e27a7b.json"}}, {"family": "Saevarsdottir", "given": "Saedis", "initials": "S"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I", "orcid": "0000-0002-4514-7706", "researcher": {"href": "https://publications.scilifelab.se/researcher/90121ddba7fe4f928c1b121b162c2509.json"}}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "Eriksson", "given": "Oskar", "initials": "O"}], "type": "journal article", "published": "2026-04-09", "journal": {"title": "Lupus Sci Med", "issn": "2053-8790", "volume": "13", "issue": "1", "issn-l": "2053-8790"}, "abstract": "SLE is a systemic autoimmune disease in which the complement system plays a key pathogenic role, yet the contribution of the lectin pathway remains unclear. Lectin pathway-dependent complement activation is initiated by pattern-recognition molecules complexed with mannose-binding lectin (MBL)-associated serine proteases (MASPs) and MBL-associated proteins (MAPs). Here, we combined biochemical and genetic analyses to explore associations between MASP/MAP proteins, SLE manifestations and autoantibody specificities.\n\nSerum concentrations of MASP-3, MAP-1 and MASP-2 were measured using ELISA in Swedish patients with SLE (n=522) and population-based matched controls (n=322). Serum type I interferon activity was measured by a cell-based reporter assay. Associations with SLE manifestations and autoantibodies were explored using logistic regression models. Single-nucleotide genetic variants spanning the MASP1 and MASP2 genes were analysed for associations with MASP/MAP levels and SLE manifestations.\n\nPatients with MAP-1 serum concentrations in the highest quartile had significantly higher rates of discoid rash (OR 2.8 (95% CI 1.4 to 5.7)), haematological manifestations (OR 2.1 (95% CI 1.1 to 3.7)) and autoantibodies against Sm, RNP, SSA and SSB (ORs 2.4 (95% CI 1.3 to 4.6) to 3.6 (95% CI 1.7 to 7.7)). Patients in the highest quartiles of MAP-1 and MASP-2 had lower rates of anti-\u03b22GP1 and anti-cardiolipin IgG and IgA anti-phospholipid antibodies (ORs 0.29 (95% CI 0.12 to 0.68) to 0.56 (95% CI 0.31 to 1.0)). Serum MAP-1 levels correlated with type I interferon activity (Spearman's rho 0.34, p<0.0001), which mediated the associations of MAP-1 with haematological manifestations and Sm/RNP autoantibodies. Significant protein quantitative trait loci for MAP-1 and MASP-2 were identified; however, these did not show consistent associations with SLE or specific SLE manifestations.\n\nThese results demonstrate a distinct clinical and serological SLE profile associated with components of the lectin pathway. The lectin pathway-regulatory protein MAP-1 displayed the strongest associations and may serve as a marker of SLE manifestations with a type I interferon signature.", "doi": "10.1136/lupus-2025-001890", "pmid": "41956715", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pii", "key": "13/1/e001890"}], "notes": [], "created": "2026-04-15T06:40:16.897Z", "modified": "2026-04-15T06:40:17.508Z"}, {"entity": "publication", "iuid": "9bc3232d9f3b460cb3a8d08f5d9bd344", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9bc3232d9f3b460cb3a8d08f5d9bd344.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9bc3232d9f3b460cb3a8d08f5d9bd344"}}, "title": "Single-cell analysis of inhibitory efferent neurons of the zebrafish lateral line.", "authors": [{"family": "Manuel", "given": "Remy", "initials": "R", "orcid": "0000-0001-6938-4864", "researcher": {"href": "https://publications.scilifelab.se/researcher/927f9373b9f44c68ab362fa91a4bb8a9.json"}}, {"family": "Ahemaiti", "given": "Aikeremu", "initials": "A"}, {"family": "Tuz-Sasik", "given": "Melek Umay", "initials": "MU", "orcid": "0000-0002-0906-7477", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf8b429a428493d8ee662e648798951.json"}}, {"family": "Boije", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2026-04-08", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "21", "issue": "4", "pages": "e0346255", "issn-l": "1932-6203"}, "abstract": "The zebrafish lateral line system is a sensory network made up of neuromasts, which contain hair cells to detect water flow. Neuromasts signal via sensory afferent neurons and their activity is modulated by efferent neurons. Inhibitory efferent neurons consist of REN, ROLE, and RELL cells and previous work has shown that neuromasts can be innervated by multiple efferent neurons, suggesting potential functional differences. To explore this, we performed single-cell RNA sequencing on REN, ROLE, and RELL neurons in 5-day-old zebrafish larvae. GO analysis across differentially expressed genes did not reveal pathways that suggest differences in cellular function. Comparing markers for neurotransmitter phenotype showed all inhibitory efferent neurons to be cholinergic, but also expressed genes related to other neurotransmitters. Expression of selected genes related to rhombomere location, axon guidance, or gap junctions was similar across efferent neurons. Expression of genes encoding proteins related to membrane potential suggest that REN neurons might be more sensitive to glutamate and may have different action potential dynamics, although functional validation remains to be done. In addition, we assessed neuromast innervation by ROLE and RELL neurons. We found that both ROLE and RELL neurons synapse to approximately 50% of hair cells within a neuromast, compared to approximately 75% innervation by all inhibitory efferent neurons combined. In addition, we did not observe flow polarity bias by innervating efferent axons. However, we did find that RELL neurons had a lower number of synaptic boutons compared to ROLE, which may reflect differences in synaptic output capacity. Taken that our transcriptional analysis did not reveal major intrinsic molecular differences, but we did observe differences in neuromast innervation, raises the possibility that functional differences, if present, may come from upstream inputs. Future work, such as retrograde tracing, could help map these input partners and clarify how different types of efferent neurons contribute to sensory modulation.", "doi": "10.1371/journal.pone.0346255", "pmid": "41950195", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13061224"}, {"db": "pii", "key": "PONE-D-25-53779"}], "notes": [], "created": "2026-04-09T11:03:25.812Z", "modified": "2026-05-27T11:38:01.833Z"}, {"entity": "publication", "iuid": "b05f9a8302e1405588f93dc3cb79e0e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b05f9a8302e1405588f93dc3cb79e0e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b05f9a8302e1405588f93dc3cb79e0e5"}}, "title": "Proviral NUP153 binding to viral proteins and RNA regulates structural-nonstructural protein ratios in orthoflavivirus infection.", "authors": [{"family": "Peters", "given": "Marie B A", "initials": "MBA", "orcid": "0000-0001-8994-0864", "researcher": {"href": "https://publications.scilifelab.se/researcher/df4733590d054742b732c2028a8f5e8a.json"}}, {"family": "Lindqvist", "given": "Richard", "initials": "R"}, {"family": "Kassa", "given": "Eszter", "initials": "E"}, {"family": "Yau", "given": "Wai-Lok", "initials": "WL"}, {"family": "Sengupta", "given": "Pallabi", "initials": "P", "orcid": "0000-0002-1413-9412", "researcher": {"href": "https://publications.scilifelab.se/researcher/851c95f648f242e0ba67202279725796.json"}}, {"family": "Niedermoser", "given": "Isabell", "initials": "I", "orcid": "0000-0002-5301-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a2b5c11f4f945a5a273c9fd040bee6f.json"}}, {"family": "Gerold", "given": "Gisa", "initials": "G", "orcid": "0000-0002-1326-5038", "researcher": {"href": "https://publications.scilifelab.se/researcher/6353493de47c4ec58831f79ed94045f4.json"}}, {"family": "Sabouri", "given": "Nasim", "initials": "N", "orcid": "0000-0002-4541-7702", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bdc688dc85a4932acfdfffad8bfc443.json"}}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}, {"family": "Lundmark", "given": "Richard", "initials": "R", "orcid": "0000-0001-9104-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e1b756caa79468dab0f960e43cd61d3.json"}}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK", "orcid": "0000-0001-6553-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/506b0e2b2d884f868df73c7663b9ffb7.json"}}], "type": "journal article", "published": "2026-04-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723"}, "abstract": "Orthoflaviviruses are RNA viruses that cause serious diseases in humans, with currently no antivirals available. Targeting host factors is emerging as an attractive antiviral approach. However, as a first step, there is a need to understand which host proteins are hijacked and for what purpose. Here, using a combination of fluorescence microscopy, knock-down, crosslinking immunoprecipitation sequencing, mass spectrometry, and in vitro and biophysical assays, we identify nucleoporin-153 (NUP153) as a proviral factor during orthoflavivirus infection. We show that NUP153 is recruited to the virus amplification site on the endoplasmic reticulum to impact the structural to nonstructural viral protein ratios. We find that NUP153 interacts with both the viral proteins NS3 and NS5, and a highly conserved G-rich motif on the viral RNA. These interactions specifically promote the production of viral structural proteins, leading to an efficient virion assembly, virus release and spread to new cells. We propose that NUP153 acts as a key regulator in viral protein ratios, a mechanism that appears conserved among orthoflaviviruses.", "doi": "10.1038/s41467-026-71449-1", "pmid": "41951628", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-026-71449-1"}], "notes": [], "created": "2026-04-10T12:13:07.525Z", "modified": "2026-04-10T12:13:08.280Z"}, {"entity": "publication", "iuid": "d28a4f21a24a4775aecb9fff4b468e8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d28a4f21a24a4775aecb9fff4b468e8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d28a4f21a24a4775aecb9fff4b468e8a"}}, "title": "Neoadjuvant palbociclib and endocrine therapy versus chemotherapy in ER + /HER2- breast cancer: a randomized phase II trial.", "authors": [{"family": "Matikas", "given": "Alexios", "initials": "A", "orcid": "0000-0002-4122-9624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0af6483a77d746c2b838414692f1f4ed.json"}}, {"family": "Tzoras", "given": "Evangelos", "initials": "E"}, {"family": "Sarafidis", "given": "Michail", "initials": "M"}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG", "orcid": "0000-0001-9919-4471", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8506000a14a4a5286aa557ab67ef690.json"}}, {"family": "Bj\u00f6hle", "given": "Judith", "initials": "J"}, {"family": "Barnekow", "given": "Elin", "initials": "E"}, {"family": "Margolin", "given": "Sara", "initials": "S"}, {"family": "Isaksson-Friman", "given": "Erika", "initials": "E"}, {"family": "Kessler", "given": "Luisa Edman", "initials": "LE"}, {"family": "Zouzos", "given": "Athanasios", "initials": "A", "orcid": "0000-0003-2654-827X", "researcher": {"href": "https://publications.scilifelab.se/researcher/776e7ba8993b4465a27451629b509490.json"}}, {"family": "Johansson", "given": "Hemming", "initials": "H"}, {"family": "Hellstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Agartz", "given": "Susanne", "initials": "S"}, {"family": "Gryb\u00e4ck", "given": "Per", "initials": "P", "orcid": "0000-0002-1141-6234", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b5986c379cd4d23a0b48ac328faab63.json"}}, {"family": "Salgkamis", "given": "Dimitrios", "initials": "D", "orcid": "0000-0002-3020-0359", "researcher": {"href": "https://publications.scilifelab.se/researcher/826836fefcf5440ebef1c404e046a0ca.json"}}, {"family": "Zerdes", "given": "Ioannis", "initials": "I", "orcid": "0000-0002-8304-2462", "researcher": {"href": "https://publications.scilifelab.se/researcher/f786763a4a0e4b5bb865ebb199eb6ca2.json"}}, {"family": "Wang", "given": "Kang", "initials": "K", "orcid": "0000-0001-5401-1803", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bdb074014224910b0f34e893b15e660.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Acs", "given": "Balazs", "initials": "B", "orcid": "0000-0002-0972-4633", "researcher": {"href": "https://publications.scilifelab.se/researcher/efe428be3caf4deca0a7839d555f6c33.json"}}, {"family": "Sun", "given": "Wenwen", "initials": "W"}, {"family": "Boyaci", "given": "Ceren", "initials": "C"}, {"family": "Villacampa", "given": "Guillermo", "initials": "G"}, {"family": "Pascual", "given": "Tomas", "initials": "T", "orcid": "0000-0001-8431-3183", "researcher": {"href": "https://publications.scilifelab.se/researcher/c10a027f0fa74b6b9a667edcadf8f50e.json"}}, {"family": "Gavila", "given": "Joaquin", "initials": "J"}, {"family": "Prat", "given": "Aleix", "initials": "A", "orcid": "0000-0003-2377-540X", "researcher": {"href": "https://publications.scilifelab.se/researcher/582dfbb079214acbb35af0a0590b2fb3.json"}}, {"family": "Perou", "given": "Charles", "initials": "C"}, {"family": "Brandberg", "given": "Yvonne", "initials": "Y"}, {"family": "Bergh", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5526-1847", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd38f4f7704144ed9e3f869e197175e6.json"}}, {"family": "Hatschek", "given": "Thomas", "initials": "T"}, {"family": "Foukakis", "given": "Theodoros", "initials": "T", "orcid": "0000-0001-8952-9987", "researcher": {"href": "https://publications.scilifelab.se/researcher/7683c0280e9b4145aa54305fb08936a7.json"}}], "type": "journal article", "published": "2026-04-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "In PREDIX LumB patients with estrogen receptor positive and human epidermal growth factor receptor negative (ER + /HER2-) breast cancer > 20 mm and/or with lymph node metastasis were randomized 1:1 to receive either paclitaxel weekly for 12 weeks followed by palbociclib and endocrine therapy for 12 weeks (arm A), or the reverse sequence (arm B). Primary endpoint is objective radiologic response at 12 weeks (ORR12), and key secondary endpoints are ORR24, pathologic complete response, event-free survival, safety and correlative studies of tissue and circulating biomarkers. Whole exome sequencing and RNA sequencing were performed on baseline fresh frozen tissue samples. In total, 179 patients comprise the intention-to-treat population. There is no statistically significant difference between the two arms in ORR12 (59% vs 45%, p = 0.058). An exploratory gene expression analysis identified differentially expressed genes and gene sets between responders and non-responders at 12 weeks. A predictive signature, CDKPredX, comprising 31 genes related to proliferation, ER signaling and immune activity was developed to identify patients resistant to chemotherapy but responding to palbociclib plus endocrine therapy (pinteraction=0.03). The predictive signature was independently validated in the CORALLEEN trial (pinteraction=0.048). Clinicaltrials.gov identifier: NCT02603679.", "doi": "10.1038/s41467-026-71452-6", "pmid": "41951647", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-026-71452-6"}, {"db": "pmc", "key": "PMC13069018"}, {"db": "ClinicalTrials.gov", "key": "NCT02603679"}], "notes": [], "created": "2026-04-13T07:03:30.099Z", "modified": "2026-04-13T07:03:31.324Z"}, {"entity": "publication", "iuid": "16a8d45180854dfdb468144fa9775e34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16a8d45180854dfdb468144fa9775e34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16a8d45180854dfdb468144fa9775e34"}}, "title": "Generalist phyllosphere taxa dominate microbial communities on macrophytes across a natural salinity gradient", "authors": [{"family": "Herlemann", "given": "Daniel P R", "initials": "DPR"}, {"family": "Riedinger", "given": "David J", "initials": "DJ"}, {"family": "Fen\u00e1ndez-Ju\u00e1rez", "given": "Victor", "initials": "V"}, {"family": "Delgado", "given": "Luis F", "initials": "LF", "orcid": "0000-0001-7850-5285", "researcher": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Pansch", "given": "Christian", "initials": "C", "orcid": "0000-0001-8442-4502", "researcher": {"href": "https://publications.scilifelab.se/researcher/50129df0120e441081efa1a9649ffbd5.json"}}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}, {"family": "Bengtsson", "given": "Mia M", "initials": "MM"}, {"family": "Gyraite", "given": "Greta", "initials": "G", "orcid": "0000-0002-7079-7997", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9fa8139fbc64e7e990587ca8e5f6d52.json"}}, {"family": "Reusch", "given": "Thorsten B H", "initials": "TBH", "orcid": "0000-0002-8961-4337", "researcher": {"href": "https://publications.scilifelab.se/researcher/39b27965acd74a7a95e97b77abee769d.json"}}, {"family": "Katarzyte", "given": "Marija", "initials": "M"}, {"family": "Kube", "given": "Sandra", "initials": "S"}, {"family": "Martin", "given": "Georg", "initials": "G", "orcid": "0000-0002-5289-6131", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fa7c61072034af188ed3685ce83ca3c.json"}}, {"family": "Rakowski", "given": "Marcin", "initials": "M"}, {"family": "Labrenz", "given": "Matthias", "initials": "M", "orcid": "0000-0003-3452-8631", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c42f1aada5411281b2bdc4d2f8e934.json"}}], "type": "journal-article", "published": "2026-04-04", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "21", "issue": "1", "issn-l": null}, "abstract": "Shallow coastal habitats are characterized by diverse macrophytes and often feature steep abiotic gradients, including salinity variations, which can shape the leaf- surface epi-microbiome (phyllosphere). To elucidate the effect of salinity and host identity on the phyllosphere of aquatic macrophytes in shallow water, we sampled the leaf surface microbiota across a salinity range of 6-15. Samples included the eelgrass Zostera marina, as well as the Eurasian water milfoil (Myriophyllum spicatum), muskgrass (Chara spp.), and sago pondweed (Stuckenia pectinata) in the brackish Baltic Sea during the summer of 2022. Microbial communities were characterized using 16S and 18S rRNA gene amplicon sequencing.\n\nAs hypothesized, the phyllosphere bacterial and protist community composition was distinct from the surrounding seawater microbiome. Typically associated taxa included the genera Loktanella, Pseudorhodobacter, the methylotrophic genus Methylotenera, unclassified Synechococcales, and Rhodobacteriaceae. Protist genera such as Picochlorum were consistently detected across all macrophyte hosts, while Cocconeis, Cyclotella, Mondous and unclassified Bacillariophyceae were present in all phyllospheres except Chara spp. Both, salinity and host species significantly influenced the composition and prevalence of the microbiota, primarily through shifts in the abundance of typical phyllosphere taxa. However, only 4-11% of phyllosphere taxa were uniquely associated with a specific salinity or macrophyte host.\n\nOur results demonstrate that aquatic macrophytes harbor a distinct and characteristic phyllosphere microbiome. The low proportion of host- or salinity specific taxa suggests that the most abundant members of this community are generalists, broadly adapted to the phyllosphere niche rather than being narrowly specialized. This implies that the presence of the macrophyte itself, providing a stable, nutrient-rich surface, exerts a stronger deterministic influence on the microbial community than the host identity or salinity fluctuations. Consequently, the phyllosphere appears relatively resilient to environmental variability, particularly salinity fluctuations. This highlights the robust nature of host-microbiome interactions and their importance for conservation of aquatic macrophyte ecosystems.", "doi": "10.1186/s40793-026-00881-z", "pmid": "41935342", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13067490"}, {"db": "pii", "key": "10.1186/s40793-026-00881-z"}], "notes": [], "created": "2026-04-10T12:05:26.160Z", "modified": "2026-04-16T09:42:39.411Z"}, {"entity": "publication", "iuid": "15e539643f51433caa47680271e70979", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15e539643f51433caa47680271e70979.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15e539643f51433caa47680271e70979"}}, "title": "Limosilactobacillus reuteri metabolites modulate immune pathways and intestinal barrier repair after 5 fluorouracil exposure.", "authors": [{"family": "Lasaviciute", "given": "Gintare", "initials": "G"}, {"family": "L\u00f3pez Plana", "given": "Marta", "initials": "M"}, {"family": "Sundberg \u00d6rtegren", "given": "Sofia", "initials": "S"}, {"family": "Telli", "given": "Sevasteia", "initials": "S"}, {"family": "Kourmoulakis", "given": "Symeon", "initials": "S"}, {"family": "Ermann Lundberg", "given": "Ludwig", "initials": "L", "orcid": "0000-0001-5983-1771", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb47fe370d24b30b505f75583167a9f.json"}}, {"family": "Lidberg", "given": "Kenny", "initials": "K"}, {"family": "Peiris", "given": "Oshadi", "initials": "O"}, {"family": "Sinha", "given": "Indranil", "initials": "I", "orcid": "0000-0002-2513-5927", "researcher": {"href": "https://publications.scilifelab.se/researcher/970cda1bb71d4ae1b36cc5628023f7d4.json"}}, {"family": "Jonsson", "given": "Ann-Beth", "initials": "AB"}, {"family": "Roos", "given": "Stefan", "initials": "S", "orcid": "0000-0002-1606-1794", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab7209c1ebe40d8bdcc73f99fb44b29.json"}}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Mata Forsberg", "given": "Manuel", "initials": "M", "orcid": "0009-0008-3711-9722", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a1120ae12e54a829e523e983c5ea0d2.json"}}, {"family": "Sverremark-Ekstr\u00f6m", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2026-04-02", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "Antimetabolites such as 5 fluorouracil are known to induce inflammation in the gut and oral cavity, underscoring the need for strategies that mitigate chemotherapy-associated toxicity. The aim of this study was to determine whether secreted components from the probiotic bacterium Limosilactobacillus reuteri DSM 17938, specifically cell-free supernatant, exopolysaccharides, and extracellular membrane vesicles, can support epithelial barrier recovery following 5 fluorouracil-induced injury. Exposure to 5 fluorouracil impaired viability, metabolic activity, and barrier integrity, and shifted the functional responses of Caco-2 cells toward increased inflammation. Stimulation with exopolysaccharides after removal of 5 fluorouracil significantly improved barrier integrity in both enterocyte-like Caco-2 cells and primary human intestinal epithelial cells, while paradoxically inducing an inflammatory protein profile in the enterocyte-like cells. Transcriptomic analysis revealed that exopolysaccharides modulate gene programs associated with extracellular matrix organization and structural remodelling. Furthermore, cell-free supernatant, membrane vesicles, and exopolysaccharides differentially influenced monocyte polarization pathways when monocytes were cultured with supernatant from 5 fluorouracil-exposed Caco-2 cells. Together, these findings demonstrate that bacterial metabolites such as exopolysaccharides influence intestinal barrier recovery upon inflammation and activate immune cell recruitment that could have consequences for the intestinal epithelial integrity during inflammation.", "doi": "10.1038/s41598-026-45524-y", "pmid": "41927663", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13049081"}, {"db": "pii", "key": "10.1038/s41598-026-45524-y"}], "notes": [], "created": "2026-04-10T12:45:16.030Z", "modified": "2026-05-04T07:55:34.771Z"}, {"entity": "publication", "iuid": "00a23e638c504441b0a54f8ee8dec96b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/00a23e638c504441b0a54f8ee8dec96b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/00a23e638c504441b0a54f8ee8dec96b"}}, "title": "Single-Cell Triomics Analysis of Tumor Cells Infiltrating Patient-Derived Breast Cancer Scaffolds", "authors": [{"family": "Filges", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5994-6699", "researcher": {"href": "https://publications.scilifelab.se/researcher/25d546bd6e774a639c45968aa81c0c1b.json"}}, {"family": "Jonasson", "given": "Emma", "initials": "E", "orcid": "0000-0003-0463-9373", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddcca3a85ea848c5afdae4d5cf066b44.json"}}, {"family": "Leiva Arrabal", "given": "Maria Del Carmen", "initials": "MDC"}, {"family": "Andersson", "given": "Lisa", "initials": "L"}, {"family": "Gustafsson", "given": "Anna", "initials": "A"}, {"family": "Dhingra", "given": "Dalia", "initials": "D"}, {"family": "Mendez", "given": "Pedro", "initials": "P"}, {"family": "Ooi", "given": "Aik", "initials": "A", "orcid": "0000-0002-9101-0372", "researcher": {"href": "https://publications.scilifelab.se/researcher/817965235259489cb9e029059b9451e3.json"}}, {"family": "Sciambi", "given": "Adam", "initials": "A"}, {"family": "Landberg", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-9004-9403", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa3b79caacba4566897f136a1200476f.json"}}, {"family": "Ruff", "given": "David", "initials": "D", "orcid": "0000-0003-2260-3163", "researcher": {"href": "https://publications.scilifelab.se/researcher/f48bd314d7494e819be6ae6d4d2ea1ca.json"}}, {"family": "St\u00e5hlberg", "given": "Anders", "initials": "A", "orcid": "0000-0003-4243-0191", "researcher": {"href": "https://publications.scilifelab.se/researcher/05306b130d6543eea88a4f518085981e.json"}}], "type": "journal-article", "published": "2026-04-00", "journal": {"title": "Am. J. Pathol.", "issn": "0002-9440", "volume": "196", "issue": "4", "pages": "1016-1027", "issn-l": null}, "abstract": "Cellular heterogeneity plays a critical role in tissues and diseases, including cancer. Single-cell technologies are required to provide detailed information about the phenotype and genotype of individual cells. Despite several approaches to analyzing different analytes at the single-cell level, it is challenging to assess DNA, RNA, and protein simultaneously. Here, a single-cell triomics method to assess DNA, RNA, and proteins from the same cell using a targeted sequencing approach is shown. Breast cancer cells cultured in monolayers and in patient-derived scaffolds that mimic in vivo-like growth conditions, both with and without chemotherapy treatment, were analyzed. Data showed that DNA, RNA, and protein biomarkers could be reliably analyzed, providing biological insights into breast cancer cell heterogeneity. In addition, chemotherapy treatment caused changes in subpopulations and expressions of biomarkers. Furthermore, cells growing in patient-derived scaffolds generated from various breast cancers affected cell heterogeneity and drug resistance differently as a result of the unique tumor-specific microenvironments. The data show that single-cell triomics provides new means to assess cancer cell heterogeneity at DNA, RNA, and protein levels.", "doi": "10.1016/j.ajpath.2025.12.013", "pmid": "41580235", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0002-9440(26)00008-8"}], "notes": [], "created": "2026-02-09T12:51:37.488Z", "modified": "2026-03-24T09:14:15.522Z"}, {"entity": "publication", "iuid": "de64661fcabe49c2a64125eae6173df5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de64661fcabe49c2a64125eae6173df5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de64661fcabe49c2a64125eae6173df5"}}, "title": "Pre-diagnostic and diagnostic D-vitamin levels and risk of bladder cancer - A nested case-control study with follow-up at diagnosis", "authors": [{"family": "Hultdin", "given": "Johan", "initials": "J", "orcid": "0000-0002-9599-0961", "researcher": {"href": "https://publications.scilifelab.se/researcher/17ea31f8b74a4a3cbbddd262227dc95d.json"}}, {"family": "Tellstr\u00f6m", "given": "Andreas", "initials": "A"}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Landstr\u00f6m", "given": "Mar\u00e9ne", "initials": "M", "orcid": "0000-0001-6737-7230", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2f02fcfb1c1497d81a6f343bc0e6928.json"}}, {"family": "Ljungberg", "given": "B\u00f6rje", "initials": "B", "orcid": "0000-0002-4121-3753", "researcher": {"href": "https://publications.scilifelab.se/researcher/36db1e6702414edfac81ab7dfa1430e9.json"}}], "type": "journal-article", "published": "2026-04-00", "journal": {"title": "Clinical Nutrition Open Science", "issn": "2667-2685", "pages": "100658", "issn-l": null}, "abstract": null, "doi": "10.1016/j.nutos.2026.100658", "pmid": null, "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-04-10T07:13:00.773Z", "modified": "2026-04-10T07:13:01.100Z"}, {"entity": "publication", "iuid": "4314ddab9c19449c8f14a8a5c00981fa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4314ddab9c19449c8f14a8a5c00981fa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4314ddab9c19449c8f14a8a5c00981fa"}}, "title": "Pan-Continental Genomic Analysis of Eurasian Perch Uncovers Global Diversity Hotspots and Postglacial Recolonization Patterns.", "authors": [{"family": "Lichman", "given": "Vitalii", "initials": "V", "orcid": "0009-0007-5955-0479", "researcher": {"href": "https://publications.scilifelab.se/researcher/379b94bfc1184a189ee57c449956ffad.json"}}, {"family": "Ozerov", "given": "Mikhail", "initials": "M"}, {"family": "L\u00f3pez", "given": "Mar\u00eda-Eugenia", "initials": "ME"}, {"family": "Noreikiene", "given": "Kristina", "initials": "K"}, {"family": "Kahar", "given": "Siim", "initials": "S"}, {"family": "Pukk", "given": "Lilian", "initials": "L"}, {"family": "Burimski", "given": "Oksana", "initials": "O"}, {"family": "Japoshvili", "given": "Bella", "initials": "B"}, {"family": "Blazhekovikj-Dimovska", "given": "Dijana", "initials": "D"}, {"family": "Lajus", "given": "Dmitry", "initials": "D"}, {"family": "Nikoli\u0107", "given": "Du\u0161an", "initials": "D"}, {"family": "Ribeiro", "given": "Filipe", "initials": "F"}, {"family": "Gebauer", "given": "Tatyana", "initials": "T"}, {"family": "Kou\u0159il", "given": "Jan", "initials": "J"}, {"family": "Peterka", "given": "Ji\u0159\u00ed", "initials": "J"}, {"family": "Blabolil", "given": "Petr", "initials": "P"}, {"family": "\u010cech", "given": "Martin", "initials": "M"}, {"family": "J\u016fza", "given": "Tom\u00e1\u0161", "initials": "T"}, {"family": "Kube\u010dka", "given": "Jan", "initials": "J"}, {"family": "Mu\u0161ka", "given": "Milan", "initials": "M"}, {"family": "\u0160mejkal", "given": "Marek", "initials": "M"}, {"family": "Va\u0161ek", "given": "Mojm\u00edr", "initials": "M"}, {"family": "Kahilainen", "given": "Kimmo", "initials": "K"}, {"family": "Lo\u017eys", "given": "Linas", "initials": "L"}, {"family": "Carlsson", "given": "Jens", "initials": "J"}, {"family": "Corcoran", "given": "William", "initials": "W"}, {"family": "Yilmaz", "given": "\u00d6zgen", "initials": "\u00d6"}, {"family": "Ekl\u00f6v", "given": "Peter", "initials": "P", "orcid": "0000-0002-8981-1453", "researcher": {"href": "https://publications.scilifelab.se/researcher/461265784bf643658985483277624d66.json"}}, {"family": "Tak\u00e1cs", "given": "P\u00e9ter", "initials": "P"}, {"family": "B\u00e1n\u00f3", "given": "B\u00e1lint", "initials": "B"}, {"family": "Pallos", "given": "R\u00e9ka", "initials": "R"}, {"family": "Kazakov", "given": "Stefan", "initials": "S"}, {"family": "Pehlivanov", "given": "Luchezar", "initials": "L"}, {"family": "Lecocq", "given": "Thomas", "initials": "T"}, {"family": "Lambert", "given": "Sophie", "initials": "S"}, {"family": "Lauridsen", "given": "Torben", "initials": "T"}, {"family": "Berthelsen", "given": "Andreas", "initials": "A"}, {"family": "Raposeiro", "given": "Pedro", "initials": "P"}, {"family": "Verreycken", "given": "Hugo", "initials": "H"}, {"family": "Britton", "given": "Robert", "initials": "R"}, {"family": "Borcheling", "given": "Jost", "initials": "J"}, {"family": "Kutsokon", "given": "Yuliia", "initials": "Y"}, {"family": "Didenko", "given": "Oleksandr", "initials": "O"}, {"family": "Jurajda", "given": "Pavel", "initials": "P"}, {"family": "Miranda", "given": "Rafael", "initials": "R", "orcid": "0000-0003-4798-314X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bb0fd0fe7d34dc4b24af564521382bd.json"}}, {"family": "Gross", "given": "Riho", "initials": "R"}, {"family": "Vasem\u00e4gi", "given": "Anti", "initials": "A"}], "type": "journal article", "published": "2026-04-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "16", "pages": "e73502", "issn-l": "2045-7758"}, "abstract": "The contemporary distribution of genetic diversity in widespread freshwater species reflects a complex interplay between historical processes and recent demographic events. We investigated the postglacial recolonization history of the Eurasian perch (Perca fluviatilis L.) across its native range spanning Europe and Western Siberia, aiming to understand how historical and recent demographic processes have shaped contemporary genetic diversity in a widespread freshwater species. Using an integrative genomic approach, we combined whole mitochondrial genome resequencing with nuclear SNP-array genotyping (3660 SNPs) for 382 individuals from 188 locations to reconstruct patterns of lineage divergence, population structure, and admixture. We identified five highly divergent mitochondrial lineages, consistent with the existence of multiple glacial refugia across Southwestern, Southeastern, and Central Europe, as well as Siberia. Nuclear data (3660 SNPs) revealed three major genetic clusters corresponding to Western, Northern, and Southeastern Europe, along with strong regional admixture. The Baltic Sea region emerged as a contemporary hotspot of genetic diversity, likely resulting from the admixture and convergence of distinct maternal lineages during the postglacial recolonization of Northern Europe. Signals of isolation by distance were evident both within and across lineages, highlighting the role of limited dispersal in shaping current genetic patterns. The integration of mitochondrial and nuclear genomic data provided a comprehensive view of the evolutionary history of P. fluviatilis, revealing both deep historical divergence and recent admixture events. The existence of multiple glacial refugia and subsequent secondary contact underscores the complexity of postglacial recolonization processes in freshwater fauna. These findings advance our understanding of how historical and contemporary factors interact to shape biodiversity across Europe.", "doi": "10.1002/ece3.73502", "pmid": "42023045", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13099172"}, {"db": "pii", "key": "ECE373502"}], "notes": [], "created": "2026-05-11T11:47:22.623Z", "modified": "2026-05-11T11:47:22.933Z"}, {"entity": "publication", "iuid": "85934359591344b9b9aa4bb18644744a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85934359591344b9b9aa4bb18644744a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85934359591344b9b9aa4bb18644744a"}}, "title": "Nasal gene expression shows a distinct signature in type 2-high asthma but not in type 2-low disease.", "authors": [{"family": "Karp", "given": "Tatiana", "initials": "T"}, {"family": "Merid", "given": "Simon Kebede", "initials": "SK"}, {"family": "Kermani", "given": "Nazanin Zounemat", "initials": "NZ"}, {"family": "Faiz", "given": "Alen", "initials": "A"}, {"family": "Gillett", "given": "Tessa E", "initials": "TE"}, {"family": "Bults", "given": "Rene", "initials": "R"}, {"family": "Raby", "given": "Katie L", "initials": "KL"}, {"family": "Kerstjens", "given": "Huib A M", "initials": "HAM"}, {"family": "Nawijn", "given": "Martijn C", "initials": "MC"}, {"family": "Piraino", "given": "Alessio", "initials": "A"}, {"family": "Kraft", "given": "Monica", "initials": "M"}, {"family": "Begh\u00e8", "given": "Bianca", "initials": "B"}, {"family": "Rabe", "given": "Klaus F", "initials": "KF"}, {"family": "Papi", "given": "Alberto", "initials": "A"}, {"family": "Brightling", "given": "Chris", "initials": "C"}, {"family": "Singh", "given": "Dave", "initials": "D"}, {"family": "Kocks", "given": "Janwillem H", "initials": "JH"}, {"family": "Siddiqui", "given": "Salman", "initials": "S"}, {"family": "Adcock", "given": "Ian M", "initials": "IM"}, {"family": "Chung", "given": "Kian Fan", "initials": "KF"}, {"family": "Bhavsar", "given": "Pankaj", "initials": "P"}, {"family": "Koppelman", "given": "Gerard H", "initials": "GH"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E"}, {"family": "Guryev", "given": "Victor", "initials": "V"}, {"family": "van den Berge", "given": "Maarten", "initials": "M"}], "type": "journal article", "published": "2026-04-00", "journal": {"title": "J. Allergy Clin. Immunol.", "issn": "1097-6825", "volume": "157", "issue": "4", "pages": "879-889", "issn-l": "0091-6749"}, "abstract": "Type 2 (T2)-low asthma is defined by low levels of T2 inflammation and is associated with resistance to inhaled corticosteroids. Its molecular mechanisms are mostly unknown, and treatment options are limited. We previously showed that nasal brush transcriptomes differ between asthma and controls, reflecting disease-relevant biology.\n\nWe explored nasal gene expression related to T2-low asthma in the ATLANTIS cohort.\n\nWe compared nasal brush RNA sequencing data between 82 T2-low and 63 T2-high asthma patients and 57 controls. T2-low asthma was defined as blood eosinophil counts < 0.15 \u00d7 109/L and Feno < 25 ppb and T2-high as blood eosinophil counts > 0.3 \u00d7 109/L and Feno > 25 ppb. Weighted gene coexpression network analysis (WGCNA) was applied to identify gene modules associated with T2-low asthma. The BAMSE and U-BIOPRED cohorts were used for replication analyses.\n\nAlthough differentially expressed genes were found in patients with T2-high asthma across all 3 cohorts, no differentially expressed genes were observed in individuals with T2-low disease compared to controls in ATLANTIS, nor consistently across other cohorts. Our assessment of molecular heterogeneity could not attribute this result to greater intersample variability within the T2-low group. WGCNA in ATLANTIS identified \"black\" and \"purple\" gene modules linked to T2-low asthma, with genes enriched in T-cell immunity and ribosomal RNA biology pathways, respectively. The \"black\" module was replicated in U-BIOPRED and showed the same direction in BAMSE.\n\nT2-high asthma shows a distinct nasal gene expression signature compared to healthy controls, while patients with T2-low asthma exhibit no consistent changes. Future studies should explore T-cell immunity in T2-low asthma and integrate lower airway multiomics data.", "doi": "10.1016/j.jaci.2025.10.036", "pmid": "41485495", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0091-6749(25)02261-4"}], "notes": [], "created": "2026-05-27T11:37:51.702Z", "modified": "2026-05-27T11:37:51.706Z"}, {"entity": "publication", "iuid": "67eb0d7fc75a45f8a47f45fc5243daa7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/67eb0d7fc75a45f8a47f45fc5243daa7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/67eb0d7fc75a45f8a47f45fc5243daa7"}}, "title": "Differential negative dominance by KCNA2 variants associated with global developmental delay suggests KCNA2 haploinsufficiency in humans.", "authors": [{"family": "Boon", "given": "Pei Xin", "initials": "PX", "orcid": "0009-0001-4366-4507", "researcher": {"href": "https://publications.scilifelab.se/researcher/d037eb59a4144be1a05c7b830a8c0929.json"}}, {"family": "Jauregi-Miguel", "given": "Amaia", "initials": "A", "orcid": "0000-0003-0938-7734", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd678c2b74f74975a83ca102fa473752.json"}}, {"family": "Yasarbas", "given": "S Suheda", "initials": "SS", "orcid": "0009-0002-8528-2539", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b15e89897e04bedaf5b070a03959a9f.json"}}, {"family": "Pozzi", "given": "Serena", "initials": "S", "orcid": "0009-0009-2688-1575", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab10411118ea486d9fa1fc348cb306cd.json"}}, {"family": "Karlsson", "given": "Urban", "initials": "U", "orcid": "0000-0002-9228-1625", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb7fa0354374416ca2f928c56f4ffe81.json"}}, {"family": "Husami", "given": "Ammar", "initials": "A", "orcid": "0000-0002-4287-2857", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ec9d6ec3af24a5bb2a163b323835d74.json"}}, {"family": "Ko", "given": "Charmaine", "initials": "C", "orcid": "0009-0003-1026-8836", "researcher": {"href": "https://publications.scilifelab.se/researcher/002ecdac5e4a4ca59b39b21ed2d10d54.json"}}, {"family": "Shillington", "given": "Amelle", "initials": "A", "orcid": "0000-0002-7447-8117", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9ab021d089429baf50a212a59ca1a8.json"}}, {"family": "Pantazis", "given": "Antonios", "initials": "A", "orcid": "0000-0002-6467-1327", "researcher": {"href": "https://publications.scilifelab.se/researcher/810aaa85bf734f03a9e25e0651b45c19.json"}}], "type": "journal article", "published": "2026-04-00", "journal": {"title": "J Physiol", "issn": "1469-7793", "volume": "604", "issue": "8", "pages": "3413-3430", "issn-l": null}, "abstract": "KCNA2 encodes the pore-forming subunits of the voltage-gated, potassium-selective channel KV1.2, which controls the excitability of both central and peripheral neurons. Either gain- or loss-of-function KCNA2 variants can cause severe neurological disease, assigned developmental epileptic encephalopathy (DEE) type 32. Here, we report and characterize two apparently similar variants, p.H310D and p.G318D, both discovered in patients with global developmental delay and involving aspartate substitutions at positions highly conserved in the KV-channel superfamily. We found that both are loss-of-function variants, completely abolishing channel current and subunit trafficking. Channel constructs of KV1.2-variant subunits in tandem with KV1.4 had a conductance with inhibited voltage-dependence, with shifted half-activation potentials by 27 and 19 mV for p.H310D and p.G318D, respectively. p.H310D was strongly negative-dominant: heterozygous cells exhibited only 7% conductance relative to homozygous wild-type, while only half of wild-type subunits could traffic to the surface. In contrast, p.G318D exhibited weaker negative dominance, with 32% conductance in heterozygous cells and 86% wild-type-subunit trafficking. Taken together with the p.G318D-patient's neurological symptoms, the latter suggests that KCNA2 is a haploinsufficient gene in humans. KEY POINTS: KCNA2 encodes the pore-forming subunits of the KV1.2 voltage-activated, K+-selective ion channel, which regulates electrical signalling in neurons. We characterized two KCNA2 variants from patients with global developmental delay. Both variants are aspartate substitutions of proximal, highly conserved positions in KV-channels: p.H310D and p.G318D. In frog oocytes and in primate cells, both variants cause loss of KCNA2 function, abolishing currents and surface trafficking, and inhibiting channel voltage-dependent opening. p.H310D is strongly negative-dominant, potently suppressing wild-type subunit functional expression. In contrast, p.G318D is weakly negative-dominant, leaving wild-type subunits largely unaffected. This suggests that KCNA2 is a haploinsufficient gene in humans.", "doi": "10.1113/JP290728", "pmid": "41914769", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Link\u00f6ping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13082188"}], "notes": [], "created": "2026-05-19T07:50:00.374Z", "modified": "2026-05-19T07:50:43.828Z"}, {"entity": "publication", "iuid": "d07dfbb5faf14d66a0758d483af8d8b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d07dfbb5faf14d66a0758d483af8d8b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d07dfbb5faf14d66a0758d483af8d8b4"}}, "title": "Bite-DNA Shows Substantial Browsing on Willows (Salix spp.) by North American Bison in Yellowstone National Park.", "authors": [{"family": "Jansson", "given": "Julia L", "initials": "JL"}, {"family": "Spitzer", "given": "Robert", "initials": "R", "orcid": "0000-0003-2753-1912", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c48a231a06f41b395bd2c7d98b2b0b2.json"}}, {"family": "Brealey", "given": "Jaelle Caitlin", "initials": "JC"}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-1246-5046", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccdce43407204828b73bce24fc4e6453.json"}}], "type": "journal article", "published": "2026-04-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "16", "issue": "4", "pages": "e73354"}, "abstract": "Riparian willows (Salix spp.) in Yellowstone National Park have long been shaped by ungulate browsing, yet the specific contribution of individual herbivore species remains unclear. We applied a bite-DNA metabarcoding approach, extracting saliva DNA from browsed willow twigs, to directly identify the browsing community across six northern range riparian sites. Mammalian DNA was successfully assigned for more than half of the collected bite samples, revealing browsing by moose (Alces alces), North American bison (Bison bison), elk (Cervus canadensis), deer (Odocoileus sp.), bighorn sheep (Ovis canadensis), and jackrabbit (Lepus townsendii). Contrary to the traditional view of bison as primarily grazers, bite-DNA showed that bison were the most frequent browsers of willows, present at all sites and contributing the majority of browsing bites. Elk, historically considered the primary browser on riparian shrubs, were detected less often, whereas mule deer browsing was consistently recorded and frequently exceeded elk. Browsing height largely overlapped among species and was significantly higher for bighorn sheep than for bison and mule deer. Diameter of browsed twigs did not differ significantly between species. Browsing composition varied locally without clear spatial patterns, suggesting that site-level factors shape where different ungulates browse willows. Our results demonstrate substantial bison browsing on riparian willows and highlight shifting herbivore impacts on Yellowstone's riparian ecosystems.", "doi": "10.1002/ece3.73354", "pmid": "42040859", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13106989"}, {"db": "pii", "key": "ECE373354"}, {"db": "Dryad", "key": "10.5061/dryad.gtht76j1w"}], "notes": [], "created": "2026-06-08T17:24:50.294Z", "modified": "2026-06-08T17:26:16.368Z"}, {"entity": "publication", "iuid": "eff23dc9016246219df7655c04dbc6c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eff23dc9016246219df7655c04dbc6c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eff23dc9016246219df7655c04dbc6c8"}}, "title": "Comparative Transcriptome Profiling of Nicotiana benthamiana Plants Infected with Potato Mop-Top Virus and Its Mutant Lacking a Gene for the 8K Protein Underlines the Role of Chloroplasts During Infection.", "authors": [{"family": "Roy", "given": "Shweta", "initials": "S"}, {"family": "Nemes", "given": "Katalin", "initials": "K"}, {"family": "Saripella", "given": "Ganapathi Varma", "initials": "GV"}, {"family": "Vetukuri", "given": "Ramesh Raju", "initials": "RR", "orcid": "0000-0001-7129-5326", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbb5fb93506a4b3a8faacc38397a741c.json"}}, {"family": "Siddique", "given": "Abu Bakar", "initials": "AB"}, {"family": "Savenkov", "given": "Eugene I", "initials": "EI", "orcid": "0000-0002-5802-5089", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e4c252bb7ec444c935c0aae5387df53.json"}}], "type": "journal article", "published": "2026-03-31", "journal": {"title": "Mol. Plant Microbe Interact.", "issn": "0894-0282", "pages": "MPMI10250146R", "issn-l": null}, "abstract": "Potato mop-top virus (PMTV) is a significant pathogen causing potato \"spraing\" disease worldwide. The PMTV 8K protein functions as a weak viral suppressor of RNA silencing (VSR), has viroporin activity, and plays a role in pathogenicity by promoting viral long-distance movement and modulating host responses. Uniquely, PMTV can establish systemic infection in the absence of the 8K protein, though the infection is slightly delayed. To elucidate the molecular mechanisms underlying PMTV-host interactions, we conducted comprehensive RNA-seq analysis comparing wild-type PMTV with a mutant lacking the 8K gene (PMTV-\u03948K) in Nicotiana benthamiana. Our transcriptomic analysis shows that wild-type PMTV and PMTV-\u03948K elicit largely distinct transcriptional responses in the host, with more unique than shared differentially expressed genes. The analysis also revealed extensive reprogramming of metabolic pathways, stress responses, and defense mechanisms. Notably, wild-type PMTV induced more defense-related transcription factors, including 27 WRKY genes compared with 8 in PMTV-\u03948K infections. RNA-silencing pathway genes displayed distinct expression patterns, with AGO2, RDR1, and AGO-MEL1 showing notably enhanced upregulation (up to 9.7-fold) in PMTV-\u03948K infections. Functional analysis identified chloroplast-associated genes GNS2, CHUP1, and KIN5l as host restriction factors. Virus-induced gene silencing experiments confirmed that GNS2 and CHUP1 restrict viral accumulation under both infection scenarios (wild-type PMTV and PMTV-\u03948K), and localization studies revealed that the TGB2 protein and GNS2 colocalize at chloroplast structures. These findings provide insights into PMTV pathogenesis, suggest that 8K is a multifunctional protein operating through diverse mechanisms, and advance understanding of viral suppression strategies. [Formula: see text] Copyright \u00a9 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.", "doi": "10.1094/MPMI-10-25-0146-R", "pmid": "41642887", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-06-01T11:10:49.177Z", "modified": "2026-06-01T11:10:49.273Z"}, {"entity": "publication", "iuid": "4841e395d0f541e6b7f8203d0fa258c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4841e395d0f541e6b7f8203d0fa258c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4841e395d0f541e6b7f8203d0fa258c0"}}, "title": "Medical facemask waste alters detritus decomposition and fungal communities in a freshwater pond.", "authors": [{"family": "Kong", "given": "Ze Hui", "initials": "ZH"}, {"family": "Stangl", "given": "Martina", "initials": "M"}, {"family": "Oester", "given": "Rebecca", "initials": "R"}, {"family": "Rehnstam", "given": "Svante", "initials": "S"}, {"family": "Futter", "given": "Martyn", "initials": "M"}, {"family": "Siddique", "given": "Abu Bakar", "initials": "AB"}, {"family": "Bundschuh", "given": "Mirco", "initials": "M"}, {"family": "Mckie", "given": "Brendan G", "initials": "BG"}], "type": "journal article", "published": "2026-03-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "Plastic pollution is an ongoing issue in freshwater ecosystems, including that generated from the spike in disposable facemask use during the COVID-19 pandemic. The degradation products of such plastic waste, including plastic leachate compounds and generation of microplastics, have the potential to affect freshwater ecosystem structure and function. We investigated the effects of facemask-derived polypropylene particles of different sizes and their leachates on fungal communities and detritus decomposition in a pond. We further investigated effects of the presence of wood shavings, used to represent a naturally-occurring, highly refractory, organic reference material. Over five weeks, leaf litter mass loss and cotton cellulose tensile strength loss were quantified weekly, and fungal biomass, community composition, and functional gene abundance at two time points. Wood shavings reduced leaf decomposition (-4.4%) relative to controls, while plastics increased decomposition of labile cotton cellulose (+ 6.6%), with the strongest effect from unleached microplastics (+ 22.7%). After 21 days, litter-associated fungal biomass was reduced by the presence of wood shavings (-20.1%) and plastics (-8.6%). Fungal communities differed between wood- and control treatments, and varied widely under plastic exposure. Our findings highlight size- and leachate-dependent effects of facemask-derived plastic particles on freshwater fungal communities and ecosystem functions, which largely contrasted with those of wood.\n\nThe online version contains supplementary material available at 10.1038/s41598-026-45795-5.", "doi": "10.1038/s41598-026-45795-5", "pmid": "41912744", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13039742"}, {"db": "pii", "key": "10.1038/s41598-026-45795-5"}], "notes": [], "created": "2026-06-01T08:43:00.886Z", "modified": "2026-06-01T08:43:00.918Z"}, {"entity": "publication", "iuid": "fecec34336824e84b6c3dd0f90675ef4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fecec34336824e84b6c3dd0f90675ef4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fecec34336824e84b6c3dd0f90675ef4"}}, "title": "Contrasting population genomic structuring of northern pike ( Esox lucius L.) in fresh\u2010 and brackish water environments: Implications for management and conservation", "authors": [{"family": "Diaz\u2010Suarez", "given": "Alfonso", "initials": "A", "orcid": "0000-0002-1726-2563", "researcher": {"href": "https://publications.scilifelab.se/researcher/51f3f9866fe543b78c91c9c62c362cdd.json"}}, {"family": "L\u00f3pez", "given": "Mar\u00eda\u2010Eugenia", "initials": "M"}, {"family": "Sundblad", "given": "G\u00f6ran", "initials": "G"}, {"family": "Vasem\u00e4gi", "given": "Anti", "initials": "A", "orcid": "0000-0002-2184-5534", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad9186f5720d493980b92869fb504cb8.json"}}], "type": "journal-article", "published": "2026-03-30", "journal": {"title": "J. Fish Biol.", "issn": "0022-1112", "issn-l": null}, "abstract": "Understanding the factors that shape population genetic structure is crucial for advancing evolutionary studies and developing effective management and conservation strategies. The northern pike (Esox lucius L.) is a top teleost predator that inhabits fresh and brackish water environments in the northern hemisphere. Pike populations in the brackish Baltic Sea typically display strong genetic structuring, with coastal sympatric populations that separate during spring for spawning in either shallow, sheltered brackish bays or in freshwater tributaries and wetlands. In contrast to the Baltic Sea, genomic structuring in freshwater environments, particularly in large lacustrine systems, remains poorly understood. To address this gap, we used restriction site-associated DNA-sequencing to assess the genetic structure and diversity of northern pike in two ecologically contrasting habitats: freshwater V\u00e4nern Lake, Sweden (8932 single nucleotide polimorphisms [SNPs]), and the brackish Baltic Sea around Saaremaa, Estonia (6899 SNPs). The results show strong genetic structuring and lower genetic diversity in brackish environment compared to the higher genetic diversity and extremely low genetic structuring observed in freshwater habitat. We found no evidence of divergent selection within environments. However, we identified 187 outlier SNPs and 62 outlier genes distinguishing the brackish and freshwater environments, potentially reflecting adaptation to salinity. Notably, several of these genes are associated with key biological processes, including osmotic stress regulation (akap13), early development (tfap2a) and pathogens response (tlr18). From a fisheries management perspective, our results indicate that the freshwater system can be managed as a single stock, while strong population structuring among Baltic coastal pike likely requires either large-scale solutions and/or population-specific fine-scale management efforts to maintain the genetic and life-history diversity among brackish coastal pike populations.", "doi": "10.1111/jfb.70417", "pmid": "41912439", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-04-10T13:09:47.227Z", "modified": "2026-04-16T09:42:58.777Z"}, {"entity": "publication", "iuid": "853fcd087cf147129106a699a63b80ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/853fcd087cf147129106a699a63b80ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/853fcd087cf147129106a699a63b80ef"}}, "title": "Tumor-infiltrating immature innate lymphoid cells in colorectal cancer are biased toward ILC1/tissue-resident NK cell differentiation.", "authors": [{"family": "Marchalot", "given": "Anne", "initials": "A", "orcid": "0000-0002-3042-8206", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b674db5dc349eaa4438563f2256290.json"}}, {"family": "Ljunggren", "given": "Malin", "initials": "M"}, {"family": "Stamper", "given": "Christopher", "initials": "C"}, {"family": "Weigel", "given": "Whitney", "initials": "W"}, {"family": "Tibbitt", "given": "Christopher Andrew", "initials": "CA"}, {"family": "Meininger", "given": "Isabel", "initials": "I"}, {"family": "Pandey", "given": "Ram Vinay", "initials": "RV"}, {"family": "Franklin", "given": "Miriam", "initials": "M", "orcid": "0000-0002-9402-9976", "researcher": {"href": "https://publications.scilifelab.se/researcher/b64100c086a644b8b1b7dd56f4f09da5.json"}}, {"family": "Bassett", "given": "John Washington", "initials": "JW"}, {"family": "Wirth", "given": "Lorenz", "initials": "L"}, {"family": "Colorectal Study Group", "given": "", "initials": ""}, {"family": "Lindforss", "given": "Ulrik", "initials": "U"}, {"family": "Jansson-Palmer", "given": "Gabriella", "initials": "G"}, {"family": "Nordenvall", "given": "Caroline", "initials": "C"}, {"family": "Mj\u00f6sberg", "given": "Jenny", "initials": "J", "orcid": "0000-0002-1119-0976", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcca878a7f314944bf1a4290cfd5d71d.json"}}], "type": "journal article", "published": "2026-03-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Peritoneal metastases (PM) occur in 10% of patients with colorectal cancer (CRC) and are linked to poor outcomes. Although dysregulated innate lymphoid cells (ILC) have been described in CRC, their function in CRC-PM remains unclear. Here, we analyze tumor samples from CRC and CRC-PM patients using single-cell RNA sequencing (11 patients), flow cytometry (8 patients) and differentiation assays (24 patients). Healthy colon, primary CRC and CRC-PM tumors are infiltrated by heterogeneous populations of ILC3, ILC2, ILC1, tissue resident (tr)NK cells and conventional (c)NK cells. Compared to healthy colons, primary CRC and CRC-PM tumors are depleted of ILC3 but enriched for ILC1, trNK cells and cNK cells. CRC and CRC-PM tumors harbor two immature ILC populations, early NK and na\u00efve (n)ILC, with nILCs being transcriptionally skewed toward ILC1 and trNK cells. Indeed, co-culture of isolated nILCs with OP9-DL1 cells induces intratumoral nILC differentiation into ILC1/trNK-like cells. These findings help understand the immune pathogenesis of CRC and CRC-PM and provide insights for future ILC1 and NK cell-based therapies.", "doi": "10.1038/s41467-026-71085-9", "pmid": "41896575", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13035902"}, {"db": "pii", "key": "10.1038/s41467-026-71085-9"}], "notes": [], "created": "2026-04-10T12:22:32.013Z", "modified": "2026-04-10T12:22:32.241Z"}, {"entity": "publication", "iuid": "bccea3aeba8b476eb4902896a66d3d62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bccea3aeba8b476eb4902896a66d3d62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bccea3aeba8b476eb4902896a66d3d62"}}, "title": "Analysis of medieval burials from Ibiza reveals genetic and pathogenic diversity during the Islamic period.", "authors": [{"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R", "orcid": "0000-0002-4173-8648", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4cefc4ed580469ba97e32c95477d485.json"}}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7355501dddb4508bf453c7c1ad9f107.json"}}, {"family": "Mas-Sandoval", "given": "Alex", "initials": "A"}, {"family": "Yaka", "given": "Reyhan", "initials": "R", "orcid": "0000-0002-9359-4391", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f685d3d3cac4dc6bfd4571041786add.json"}}, {"family": "Fortes-Lima", "given": "Cesar A", "initials": "CA", "orcid": "0000-0002-9310-5009", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a1afb9addfa42b4aa92a74ed8a8586b.json"}}, {"family": "Garc\u00eda Rubio", "given": "Almudena", "initials": "A"}, {"family": "M\u00e1rquez-Grant", "given": "Nicholas", "initials": "N"}, {"family": "Mar\u00ed", "given": "Juanjo", "initials": "J"}, {"family": "Graziani", "given": "Glenda", "initials": "G"}, {"family": "Ferrer Ab\u00e1rzuza", "given": "Antoni", "initials": "A"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Lorca-Francisco", "given": "Lander", "initials": "L", "orcid": "0009-0000-5486-1509", "researcher": {"href": "https://publications.scilifelab.se/researcher/306a8399107a4c078493180672a3a1b7.json"}}, {"family": "Linderholm", "given": "Anna", "initials": "A", "orcid": "0000-0002-1613-9926", "researcher": {"href": "https://publications.scilifelab.se/researcher/27c319330d1e4827858b5612dc203c69.json"}}, {"family": "Lagerholm", "given": "Vendela K", "initials": "VK"}, {"family": "Arauna", "given": "Lara R", "initials": "LR", "orcid": "0000-0003-3317-4261", "researcher": {"href": "https://publications.scilifelab.se/researcher/111d8114dc6f448c9516f8f246ef7925.json"}}, {"family": "P\u00e9rez-Ramallo", "given": "Patxi", "initials": "P", "orcid": "0000-0002-1142-4912", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cb111a8997c4fc4a3167bbeabcac042.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2026-03-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Ibiza, an island in present-day Spain, was conquered in 902 CE by the Umayyad Emirate of C\u00f3rdoba. The island remained under Islamic rule until 1235. Here, we analyse the genetic and metagenomic profiles of 13 individuals from an Islamic cemetery in Ibiza, dated to 950-1150 CE. Genome-wide analyses reveal heterogeneity, with ancestry components from Europe, North Africa, and Sub-Saharan Africa. Our analyses estimate that North African gene flow occurred two to seven generations before these individuals lived, suggesting admixture following the Islamic conquest of Iberia and potentially on Ibiza itself. Notably, two individuals trace their Sub-Saharan origins to distinct regions, Senegambia and present-day southern Chad, providing direct evidence of trans-Saharan connections via military and slave networks documented in contemporary Arabic sources. Metagenomic analyses detect several pathogens in this community, with one individual carrying Mycobacterium leprae, offering insight into the presence of leprosy in Ibiza. Our findings align with the historically documented two-pulse demographic model, indicating an initial settlement following the early tenth-century conquest and a second influx associated with Almoravid movements in the twelfth century. These securely dated genomes offer insights into medieval population dynamics and health in the Balearics.", "doi": "10.1038/s41467-026-70615-9", "pmid": "41888119", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13021928"}, {"db": "pii", "key": "10.1038/s41467-026-70615-9"}], "notes": [], "created": "2026-04-10T12:08:45.109Z", "modified": "2026-04-10T12:08:45.877Z"}, {"entity": "publication", "iuid": "af8e8e9ebf9c485889bde183fd55210f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af8e8e9ebf9c485889bde183fd55210f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af8e8e9ebf9c485889bde183fd55210f"}}, "title": "Temporal genomics reveals widespread but unexpected consequences of a bottleneck in the Scandinavian brown bear", "authors": [{"family": "Lindahl", "given": "Amanda", "initials": "A"}, {"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}, {"family": "Ravasini", "given": "Francesco", "initials": "F"}, {"family": "Meleg", "given": "Ioana N", "initials": "IN", "orcid": "0000-0002-0836-4971", "researcher": {"href": "https://publications.scilifelab.se/researcher/01e901f9e2924bee8e3de6bfbcd8fe62.json"}}, {"family": "Xenikoudakis", "given": "Georgios", "initials": "G", "orcid": "0000-0001-6929-4869", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0d428a542d44a829e17924e94a3f6dc.json"}}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}}, {"family": "Sharif", "given": "Bilal", "initials": "B"}, {"family": "Skoglund", "given": "Pontus", "initials": "P", "orcid": "0000-0002-3021-5913", "researcher": {"href": "https://publications.scilifelab.se/researcher/338a5f8f37fb48b3887230dfd81786d3.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Feinauer", "given": "Isabelle Sofie", "initials": "IS", "orcid": "0009-0004-4615-0810", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d95245a50e408a9643a18b7c0fc3d2.json"}}], "type": "journal-article", "published": "2026-03-25", "journal": {"title": "R. Soc. open sci.", "issn": "2054-5703", "issn-l": "2054-5703", "volume": "13", "issue": "3", "pages": null}, "abstract": null, "doi": "10.1098/rsos.251947", "pmid": null, "labels": {"Ancient DNA": "Collaborative", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-03-26T13:53:56.827Z", "modified": "2026-04-16T09:43:31.467Z"}, {"entity": "publication", "iuid": "23158676211240e2a69a681a1b190fe0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23158676211240e2a69a681a1b190fe0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23158676211240e2a69a681a1b190fe0"}}, "title": "Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing", "authors": [{"family": "Bilgrav Saether", "given": "Kristine", "initials": "K"}, {"family": "Salazar Mantero", "given": "Angelo", "initials": "A"}, {"family": "Ek", "given": "Marlene", "initials": "M"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Syk Lundberg", "given": "Elisabeth", "initials": "E"}, {"family": "Grochowski", "given": "Christopher M", "initials": "CM", "orcid": "0000-0002-3884-7720", "researcher": {"href": "https://publications.scilifelab.se/researcher/c94bd6d4a43e41f2990ae8b9426c0312.json"}}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB", "orcid": "0000-0002-2090-298X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1a6b6936aa442384c5aef0eff0715a.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}], "type": "journal-article", "published": "2026-03-25", "journal": {"title": "Genome Res.", "issn": "1088-9051", "volume": "36", "issue": "4", "pages": "661-670", "issn-l": null}, "abstract": "Small supernumerary marker chromosomes (sSMCs) remain a diagnostic challenge despite sequencing advances. As the field shifts toward cytogenomics, there is a need to establish methodologies to resolve these complex genetic variants at base pair resolution, as well as to identify their chromosomal origin and formation mechanism. Here, we apply long-read genome sequencing (lrGS) in combination with the telomere-to-telomere (T2T-CHM13) assembly to characterize the structure and genomic content of 10 clinically detected sSMCs. We use sequencing data to reconstruct the derivative chromosomes, identify breakpoint junctions (BPJs), and infer formation mechanisms. We resolve the BPJs of nine of the 10 sSMCs at base pair resolution. The analysis reveals six simple intrachromosomal rearrangements (one continuous and five discontinuous) with one to three BPJs, one complex three-way translocation with two BPJs, and two highly complex intrachromosomal rearrangements with five and nine BPJs, respectively. Breakpoint analysis reveals distinct mechanistic signatures: Simple sSMCs show features consistent with microhomology-mediated end joining (MMEJ) or microhomology-mediated break-induced replication (MMBIR), whereas complex sSMCs demonstrate evidence of translocation, chromoanasynthesis, and breakage-fusion-bridge (BFB) cycles. Haplotype analysis supports trisomy rescue in four cases, including all three complex sSMCs. In summary, our study demonstrates that lrGS combined with T2T-CHM13 enables detailed structural and mechanistic characterization of sSMCs, providing experimental support for disruption of trisomy rescue as a key formation mechanism. This work illustrates the feasibility of resolving highly challenging chromosomal abnormalities using long-read sequencing technologies.", "doi": "10.1101/gr.281175.125", "pmid": "41881544", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "gr.281175.125"}], "notes": [], "created": "2026-04-10T11:53:57.469Z", "modified": "2026-04-14T14:01:40.457Z"}, {"entity": "publication", "iuid": "197e14d7b03a454986e241aada0526a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/197e14d7b03a454986e241aada0526a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/197e14d7b03a454986e241aada0526a6"}}, "title": "Studying Macromolecular Composition in Cell-Cell Interfaces Using 3D Membrane Reconstitution Systems.", "authors": [{"family": "Ragaller", "given": "Franziska", "initials": "F", "orcid": "0000-0002-4148-262X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ead87aca17f476b9febf3f020567c4b.json"}}, {"family": "Schneider", "given": "Amelie Maribel", "initials": "AM"}, {"family": "Sjule", "given": "Ellen", "initials": "E"}, {"family": "Sun", "given": "Renhua", "initials": "R"}, {"family": "Han", "given": "Xiao", "initials": "X"}, {"family": "Andronico", "given": "Luca", "initials": "L", "orcid": "0000-0002-4326-073X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8818b25185e54c7e9f120d34c1fc69cd.json"}}, {"family": "Jenkins", "given": "Edward", "initials": "E"}, {"family": "Dustin", "given": "Michael", "initials": "M"}, {"family": "Achour", "given": "Adnane", "initials": "A"}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}], "type": "journal article", "published": "2026-03-24", "journal": {"title": "Adv Sci (Weinh)", "issn": "2198-3844", "pages": "e22443", "issn-l": null}, "abstract": "During direct communication between two cells, the plasma membranes of each cell serve as a platform for ligand-receptor interaction initiating downstream signaling cascades. In immune cell signaling, this cell-cell interface - the immune synapse - is highly spatiotemporally organized. Multiple stimulatory and co-stimulatory signals need to be integrated over time to ensure proper immune cell function. This process is still not fully understood given the vast complexity of interactions between proteins, lipids, glycocalyx and associated cortical actin cytoskeleton. Here, we presented a fully artificial model system to study the interface between two vesicles and a semi-artificial one between a live cell and a vesicle to reconstitute 3D contacts. We investigated the distribution and reorganization of immune cell proteins at artificial and semi-artificial contacts. We show the enrichment and depletion of different proteins in the synapse and how different peptides with varying affinity presented by the same MHC class I affect T cell activation. We further explored the distribution of glycocalyx elements and showed differential partitioning of different sugar moieties in the interface. While we focused on the T cell interface here, our model systems are powerful tools to study the distribution and reorganization of lipids, proteins and glycocalyx components at any cell-cell contact.", "doi": "10.1002/advs.202522443", "pmid": "41874480", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [], "notes": [], "created": "2026-03-26T19:13:29.629Z", "modified": "2026-03-26T19:13:29.781Z"}, {"entity": "publication", "iuid": "dcc99177f164437e8a1a681594fa0445", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dcc99177f164437e8a1a681594fa0445.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dcc99177f164437e8a1a681594fa0445"}}, "title": "Ribonuclease 4 Functions in Nociceptor-Mediated Nerve Homeostasis.", "authors": [{"family": "Feng", "given": "Xiaona", "initials": "X", "orcid": "0000-0001-6186-1160", "researcher": {"href": "https://publications.scilifelab.se/researcher/ade5499e48344e448626eef177bf1b27.json"}}, {"family": "Zhang", "given": "Kaiwen", "initials": "K", "orcid": "0009-0001-0790-1616", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1880c8da747467795a011858ca2c9bf.json"}}, {"family": "Techameena", "given": "Prach", "initials": "P", "orcid": "0009-0005-9380-2428", "researcher": {"href": "https://publications.scilifelab.se/researcher/835cc139cbbd4e08afd433a817f74ac6.json"}}, {"family": "Quadros", "given": "Rolen M", "initials": "RM"}, {"family": "Adori", "given": "Csaba", "initials": "C"}, {"family": "Murtazina", "given": "Aliia", "initials": "A"}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}, {"family": "Biagini", "given": "Sofia", "initials": "S", "orcid": "0009-0001-8033-1568", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6a1c687a2e945c0a01cd9ea4729fcd0.json"}}, {"family": "Bayramlik", "given": "Ozun Gokce", "initials": "OG", "orcid": "0009-0006-2130-9674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecf0118536354092bddc54ca48594444.json"}}, {"family": "Lallemend", "given": "Francois", "initials": "F", "orcid": "0000-0001-5484-0011", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a9494a8ea444facbf3b564670930ab5.json"}}, {"family": "Gurumurthy", "given": "Channabasavaiah B", "initials": "CB"}, {"family": "Hadjab", "given": "Saida", "initials": "S", "orcid": "0000-0001-7953-8396", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed79ab77088f43859e11b75dcae33d73.json"}}], "type": "journal article", "published": "2026-03-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "The regulation of nociceptor identity and function is essential, as disruptions can significantly influence pain sensation, yet our understanding of the molecular mechanisms involved remains incomplete. In this study, we identified ribonuclease 4 (RNase4) as selectively expressed in the unmyelinated nociceptor lineage. Analysis of RNase4-deficient mice and single-cell transcriptomic data revealed a cell-autonomous role for RNase4 in regulating nociceptor function. Moreover, in a neuropathic pain model, RNase4 expression was upregulated in nociceptors during the pain and recovery phases, and its deletion altered mechanical sensation. Additionally, RNase4 exerted non-cell- autonomous effects on the myelin structural organization of adjacent myelinated axons. Together, these findings implicate RNase4 as a dual regulator of nociceptor biology and myelin integrity, revealing a molecular pathway for pain regulation and nerve repair.", "doi": "10.1038/s41467-026-70365-8", "pmid": "41876491", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13022371"}, {"db": "pii", "key": "10.1038/s41467-026-70365-8"}], "notes": [], "created": "2026-04-10T12:49:18.049Z", "modified": "2026-04-10T12:49:18.431Z"}, {"entity": "publication", "iuid": "51ab6bef0c294812a1af87272c18bba2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51ab6bef0c294812a1af87272c18bba2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51ab6bef0c294812a1af87272c18bba2"}}, "title": "Genetic predisposition to coffee consumption and the association with the early risk of atherosclerosis.", "authors": [{"family": "Qiao", "given": "Xiangyu", "initials": "X"}, {"family": "Toma", "given": "Vanessa William", "initials": "VW"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Herraiz-Adillo", "given": "\u00c1ngel", "initials": "\u00c1"}, {"family": "S\u00f6derholm", "given": "Simon", "initials": "S"}, {"family": "Berglind", "given": "Daniel", "initials": "D"}, {"family": "Calling", "given": "Susanna", "initials": "S"}, {"family": "Daka", "given": "Bledar", "initials": "B"}, {"family": "Martinell", "given": "Mats", "initials": "M"}, {"family": "Bergman", "given": "Frida", "initials": "F"}, {"family": "Henriksson", "given": "Pontus", "initials": "P"}, {"family": "Ghafouri", "given": "Bijar", "initials": "B"}, {"family": "Ulander", "given": "Martin", "initials": "M"}, {"family": "\u00d6stgren", "given": "Carl Johan", "initials": "CJ"}, {"family": "Cant\u00f9", "given": "Claudio", "initials": "C"}, {"family": "Zhong", "given": "Wen", "initials": "W"}, {"family": "Iredahl", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2026-03-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "The cardiovascular effects of coffee consumption remain debated, particularly regarding early-stage subclinical atherosclerosis. This study investigated the association between coffee intake, genetic predisposition, and the risk of subclinical coronary and carotid atherosclerosis in 24,835 participants from the Swedish CArdioPulmonary bioImage Study (SCAPIS). Coffee intake was assessed via self-reported questionnaires. Atherosclerosis was assessed via segment involvement score (SIS), coronary artery calcium score (CACS) and carotid plaque. Observational analysis showed no significant association between coffee consumption and SIS, CACS, or carotid plaques. However, both one-sample and two-sample (SCAPIS and UK Biobank) Mendelian randomization (MR) analyses showed an association between genetic predisposition to higher coffee consumption and increased SIS. Stratification analyses further explored differences in genetic associations across varying coffee consumption levels. Among individuals consuming coffee more than twice daily, two coffee consumption-associated single nucleotide polymorphisms (SNPs) in AHR and CYP1A1/CYP1A2 were correlated with SIS. Integrative metabolomics and proteomics analyses identified lipid-related metabolites (triglycerides, phospholipids, free cholesterol) and inflammation-related proteins (DLK1, IL1RL2, CCL17) associated with the genetic proxy of coffee consumption. These findings suggest that genetically influenced coffee consumption may be associated with coronary atherosclerosis risk in frequent coffee drinkers, although the underlying biological basis remains to be clarified.", "doi": "10.1038/s41598-026-44122-2", "pmid": "41865070", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13009213"}, {"db": "pii", "key": "10.1038/s41598-026-44122-2"}], "notes": [], "created": "2026-06-01T08:45:44.894Z", "modified": "2026-06-01T08:45:44.897Z"}, {"entity": "publication", "iuid": "872c7a106b1e474792fbaa94e504a7ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/872c7a106b1e474792fbaa94e504a7ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/872c7a106b1e474792fbaa94e504a7ca"}}, "title": "Avoiding Mitochondrial Apoptosis by the Bcl-2-Driven Bax Oligomerization on Membrane Surfaces", "authors": [{"family": "Ayscough", "given": "Sophie E", "initials": "SE"}, {"family": "Clifton", "given": "Luke A", "initials": "LA", "orcid": "0000-0001-8754-362X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e26f83508bc7451a9d66123eb9ea747c.json"}}, {"family": "\u00c5d\u00e9n", "given": "J\u00f6rgen", "initials": "J", "orcid": "0000-0002-4480-1219", "researcher": {"href": "https://publications.scilifelab.se/researcher/00206abad0de45eb90dc6bd3d5f3cf22.json"}}, {"family": "K\u00f6hler", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-9707-9023", "researcher": {"href": "https://publications.scilifelab.se/researcher/955fd789119a4e5f9ec314275095a70e.json"}}, {"family": "Paracini", "given": "Nicol\u00f2", "initials": "N", "orcid": "0000-0003-3178-4867", "researcher": {"href": "https://publications.scilifelab.se/researcher/640d007b304247b9bebd4837bdeba788.json"}}, {"family": "Doutch", "given": "James", "initials": "J", "orcid": "0000-0003-0747-8368", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e1b2f6a54554068b76215bdc2554b61.json"}}, {"family": "Bragginton", "given": "\u00c9il\u00eds C", "initials": "\u00c9C"}, {"family": "Leung", "given": "Anna E", "initials": "AE", "orcid": "0000-0002-8196-9774", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f083dbf21ad4cdbbbea7248331949bf.json"}}, {"family": "Bogojevic", "given": "Oliver", "initials": "O"}, {"family": "Poon", "given": "Jia Fei", "initials": "JF", "orcid": "0000-0002-5568-7415", "researcher": {"href": "https://publications.scilifelab.se/researcher/743b924c930841eea6c30fddd62f7a10.json"}}, {"family": "Nagy", "given": "Tam\u00e1s Mil\u00e1n", "initials": "TM", "orcid": "0000-0003-4766-1992", "researcher": {"href": "https://publications.scilifelab.se/researcher/22a9fd6e6a4e46b2ae2bc0166f62e092.json"}}, {"family": "Wacklin-Knecht", "given": "Hanna P", "initials": "HP", "orcid": "0000-0002-5248-1147", "researcher": {"href": "https://publications.scilifelab.se/researcher/962e09a261294bcea30f21ae45b23177.json"}}, {"family": "Gr\u00f6bner", "given": "Gerhard", "initials": "G", "orcid": "0000-0001-7380-8797", "researcher": {"href": "https://publications.scilifelab.se/researcher/85bd86ebc85d4653bc880bc9be25bc80.json"}}], "type": "journal-article", "published": "2026-03-20", "journal": {"title": "ACS Chem. Biol.", "issn": "1554-8929", "volume": "21", "issue": "3", "pages": "565-576", "issn-l": null}, "abstract": "The Bcl-2 family of proteins governs mitochondrial outer membrane (MOM) permeabilization, a critical step in apoptosis that is dysfunctional in many cancers. Although cellular studies have long implicated direct interactions between the pore-forming apoptotic Bax protein and its opponent, the antiapoptotic Bcl-2 protein in apoptosis regulation, the underlying basic principles behind this control remained unresolved. To provide in-depth insight, we carried out a systematic biophysical study in which we utilized neutron reflectometry (NR) and ATR-FTIR to elucidate the molecular communication between those proteins in and around the mitochondrial membrane environment. The spatial and temporal changes across model MOM surfaces were resolved during the interaction of Bax with Bcl-2. The NR-derived membrane surface Bax distributions suggested that Bcl-2 mediated Bax sequestration through both Bcl-2/Bax heterodimerization and Bax/Bax oligomerization. Kinetic analysis revealed a two-step process: rapid formation of Bcl-2/Bax heterodimers, followed by slower Bax oligomerization on these complexes. Importantly, this sequestration mechanism was also observed in the presence of cardiolipin, a lipid known to promote the formation of an apoptotic pore by Bax in the absence of Bcl-2. These findings suggest a fundamental mechanism by which cancer cells may evade apoptosis by exploiting Bcl-2's ability to neutralize Bax through structural entrapment, even if excess Bax is present, either in response to treatment or natural death signals.", "doi": "10.1021/acschembio.5c00913", "pmid": "41705766", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-03-06T09:26:31.753Z", "modified": "2026-03-24T09:09:22.716Z"}, {"entity": "publication", "iuid": "b2a677b49fcd4cea828daa238d38fc87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b2a677b49fcd4cea828daa238d38fc87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b2a677b49fcd4cea828daa238d38fc87"}}, "title": "Transcription factor NFYA directs male meiotic entry by regulating accessible chromatin at meiotic promoters in mice", "authors": [{"family": "S\u00e4flund", "given": "Martin", "initials": "M", "orcid": "0009-0004-0450-1088", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2621fb0a17c498b8ea57d8db518c544.json"}}, {"family": "Askari", "given": "Masomeh", "initials": "M"}, {"family": "Eghbali", "given": "Atiyeh", "initials": "A"}, {"family": "Abdi", "given": "Mukhtar Mohamed", "initials": "MM", "orcid": "0009-0008-9207-7705", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ccfcd44f2d045338ebaff37a4481e01.json"}}, {"family": "Er", "given": "Dilay Deren", "initials": "DD", "orcid": "0009-0000-2441-5874", "researcher": {"href": "https://publications.scilifelab.se/researcher/72ed4229936e4ddeb92c9af2b029ff11.json"}}, {"family": "\u00d6stlund Farrants", "given": "Ann Kristin", "initials": "AK", "orcid": "0000-0001-9225-3264", "researcher": {"href": "https://publications.scilifelab.se/researcher/f39df17c335240939cad1d413beb13b0.json"}}, {"family": "Yu", "given": "Tianxiong", "initials": "T", "orcid": "0000-0003-1151-4624", "researcher": {"href": "https://publications.scilifelab.se/researcher/921557bbdcf34a1c822995b09d2700ea.json"}}, {"family": "\u00d6zata", "given": "Deniz M", "initials": "DM", "orcid": "0000-0001-5215-8684", "researcher": {"href": "https://publications.scilifelab.se/researcher/933850bed34c4517b01e915cf8831686.json"}}], "type": "journal-article", "published": "2026-03-19", "journal": {"title": "EMBO J.", "issn": "1460-2075", "issn-l": "0261-4189"}, "abstract": "Meiotic prophase I, characterized by homologous recombination and synapsis, is a critical step in spermatogenesis. This process entails extensive changes to chromatin and transcription. Prior to prophase I, accessible chromatin bound by paused Pol II at meiotic gene promoters is essential for their timely activation later during meiosis. However, the factors responsible for establishing accessible chromatin at meiotic gene promoters before entry into prophase I are unknown. Here, we discovered that NFYA, expressed in pre-meiotic germ cells, regulates accessible chromatin at meiotic gene promoters, including those activated by the STRA8/MEISON axis. Concordantly, conditional germline deletion of Nfya in male mice blocks meiotic entry. Single-cell ATAC-seq analysis shows that loss of NFYA in pre-meiotic cells disrupts accessible chromatin at poised meiotic gene promoters. These findings establish NFYA as a regulator of accessible chromatin at meiotic gene promoters and of the timely activation of the meiotic genetic program.", "doi": "10.1038/s44318-026-00756-6", "pmid": "41857150", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s44318-026-00756-6"}], "notes": [], "created": "2026-03-23T13:24:24.304Z", "modified": "2026-03-24T09:12:12.298Z"}, {"entity": "publication", "iuid": "59eca9ec25b940089924c25b003d94a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59eca9ec25b940089924c25b003d94a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59eca9ec25b940089924c25b003d94a3"}}, "title": "Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs.", "authors": [{"family": "Kabbe", "given": "Mukund", "initials": "M"}, {"family": "Agirre", "given": "Eneritz", "initials": "E", "orcid": "0000-0002-5012-0305", "researcher": {"href": "https://publications.scilifelab.se/researcher/a507b19745c64c3bb8ef5dce800c8687.json"}}, {"family": "Carlstr\u00f6m", "given": "Karl E", "initials": "KE", "orcid": "0000-0002-3001-2403", "researcher": {"href": "https://publications.scilifelab.se/researcher/3aa5f65acad34b5790a2b9f607521825.json"}}, {"family": "Dumral", "given": "\u00d6zge", "initials": "\u00d6", "orcid": "0000-0002-9980-2702", "researcher": {"href": "https://publications.scilifelab.se/researcher/8288edd47f70479e93e1fc441d486997.json"}}, {"family": "Lor", "given": "Yuk Kit", "initials": "YK"}, {"family": "Pohl", "given": "Fabio Baldivia", "initials": "FB", "orcid": "0000-0003-1695-4936", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7913023dd124c8f96f5d072af0eff56.json"}}, {"family": "Ruffin", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3698-5505", "researcher": {"href": "https://publications.scilifelab.se/researcher/991af3c2719f4c0b9d4feeae24c5161a.json"}}, {"family": "van Bruggen", "given": "David", "initials": "D"}, {"family": "Meijer", "given": "Mandy", "initials": "M"}, {"family": "Seeker", "given": "Luise A", "initials": "LA"}, {"family": "Bestard-Cuche", "given": "Nadine", "initials": "N"}, {"family": "Lederer", "given": "Alex R", "initials": "AR", "orcid": "0000-0001-6381-5088", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa3aa57bbddf4845b2d2c438ecfb2bff.json"}}, {"family": "Zhang", "given": "Jilin", "initials": "J"}, {"family": "Ahola", "given": "Virpi", "initials": "V"}, {"family": "Goldman", "given": "Steven A", "initials": "SA"}, {"family": "Edstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Arvidsson", "given": "Lisa", "initials": "L", "orcid": "0000-0003-2129-5357", "researcher": {"href": "https://publications.scilifelab.se/researcher/654ca67f559842669ed19aefa16f878b.json"}}, {"family": "Moreira", "given": "Tiago Holm", "initials": "TH"}, {"family": "Bartosovic", "given": "Marek", "initials": "M", "orcid": "0000-0003-2057-6050", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce3c36916eb844e7bc10f73b95f6494a.json"}}, {"family": "Jagodic", "given": "Maja", "initials": "M", "orcid": "0000-0003-0756-889X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b651ef39c6b0436992e2305f425eba72.json"}}, {"family": "Williams", "given": "Anna", "initials": "A", "orcid": "0000-0002-6329-382X", "researcher": {"href": "https://publications.scilifelab.se/researcher/80c29c92194a4af3a6ed8f9d18dbddfe.json"}}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}], "type": "journal article", "published": "2026-03-19", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256"}, "abstract": "Neural cells in the adult human central nervous system (CNS) display extensive transcriptional heterogeneity. How different layers of epigenetic regulation underpin this heterogeneity is poorly understood. Here we profile, at the single-nuclei epigenomic level, distinct regions of the adult human CNS, for chromatin accessibility and simultaneously for the histone modifications H3K27me3 and H3K27ac. We unveil a putative SOX10 enhancer and primed chromatin signatures at HOX loci in spinal-cord-derived human oligodendroglia (OLG) and astrocytes, but not microglia. These signatures in adult OLG were reminiscent of developmental profiles but were decoupled from robust gene expression. Moreover, using high-resolution Micro-C, we show that induced pluripotent stem-cell-derived human OLGs exhibit a HOX chromatin architecture compatible with the primed chromatin in adult OLGs, bearing a strong resemblance not only to OLG developmental architecture but also to high-grade pontine gliomas. Thus, epigenetic memory from developmental states in adult OLG not only enables them to promptly transcribe Hox family genes during regeneration but also makes them susceptible to gliomagenesis.", "doi": "10.1038/s41593-026-02208-0", "pmid": "41857393", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-026-02208-0"}], "notes": [], "created": "2026-03-23T13:16:33.192Z", "modified": "2026-03-23T13:16:34.150Z"}, {"entity": "publication", "iuid": "2253e344ebd94022a1be7f7534701531", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2253e344ebd94022a1be7f7534701531.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2253e344ebd94022a1be7f7534701531"}}, "title": "Sex chromosome evolution mediated by a large inversion and a possible switch of the sex determination gene.", "authors": [{"family": "Mao", "given": "Xiaomeng", "initials": "X"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Karrenberg", "given": "Sophie", "initials": "S"}], "type": "journal article", "published": "2026-03-19", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "27", "issue": "1", "issn-l": "1474-7596"}, "abstract": "Sex chromosomes often evolve faster than autosomes and commonly degenerate after recombination arrest. However, the underlying evolutionary processes are under persistent debate. In particular, it is unclear whether or not recombination arrest generally evolves in a stepwise manner and how switches in sex determination genes contribute to sex chromosome evolution. Here, we investigate sex chromosome evolution in the dioecious plant genus Salix.\n\nWe identify Z- and W-regions (~ 8 Mb) on chromosome 15 of the dwarf willow Salix herbacea using a new haplotype-resolved assembly. The W-region harbours a large (5 Mb) embedded inversion. Analyses of synteny with other Salix species, sequence divergence between sex chromosomes and sequence degeneration suggest that this inversion recently incorporated pseudoautosomal sequence into the W-region, extending its length nearly three-fold. The W-region exclusively contains seven pairs of inverted partial repeats of the male essential floral identity gene PISTILLATA, suggesting a possible PISTILLATA suppression mechanism by interfering RNA in females. Such PISTILLATA pseudogenes are also found in other Salix species with ZW sex determination but not in those with XY sex determination.\n\nOur study provides rare and compelling support for the long-standing theory of inversions underlying stepwise recombination reduction and raises the hypothesis that the turnover of sex chromosomes in the Salicaceae family might be associated with a switch of the sex determination gene.", "doi": "10.1186/s13059-026-04038-6", "pmid": "41857659", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13064059"}, {"db": "pii", "key": "10.1186/s13059-026-04038-6"}], "notes": [], "created": "2026-04-10T06:39:04.743Z", "modified": "2026-06-01T08:43:03.337Z"}, {"entity": "publication", "iuid": "68c40116843b453da94e62baf7c5a450", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68c40116843b453da94e62baf7c5a450.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68c40116843b453da94e62baf7c5a450"}}, "title": "Mapping the human chemical exposome for public health", "authors": [{"family": "David", "given": "Arthur", "initials": "A"}, {"family": "Lennon", "given": "Sarah", "initials": "S", "orcid": "0000-0001-5095-0141", "researcher": {"href": "https://publications.scilifelab.se/researcher/d35156fba141498fb1dc4dce125d22d4.json"}}, {"family": "Mercier", "given": "Fabien", "initials": "F", "orcid": "0000-0002-9523-4277", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b3d49de0f9a4e1b87a7cc409167c5ca.json"}}, {"family": "Bouhlel", "given": "Jihene", "initials": "J"}, {"family": "Chaker", "given": "Jade", "initials": "J"}, {"family": "Appenzeller", "given": "Brice M R", "initials": "BMR"}, {"family": "Audouze", "given": "Karine", "initials": "K"}, {"family": "Ayeni", "given": "Kolawole I", "initials": "KI"}, {"family": "Bailly-Chouriberry", "given": "Ludovic", "initials": "L"}, {"family": "El Balkhi", "given": "Souleiman", "initials": "S", "orcid": "0000-0002-9743-5603", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc15209068e4436f81907312dcf144fe.json"}}, {"family": "Barouki", "given": "Robert", "initials": "R"}, {"family": "Belova", "given": "Lidia", "initials": "L"}, {"family": "Benmarhnia", "given": "Tarik", "initials": "T"}, {"family": "Bonnefille", "given": "B\u00e9nilde", "initials": "B", "orcid": "0000-0001-5141-7111", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb5cae7e57b1443a8b296824dc186b04.json"}}, {"family": "Bessonneau", "given": "Vincent", "initials": "V"}, {"family": "Bonvallot", "given": "Nathalie", "initials": "N"}, {"family": "Bouchart", "given": "Val\u00e9rie", "initials": "V"}, {"family": "Bouvier-Capely", "given": "C\u00e9line", "initials": "C", "orcid": "0000-0002-8794-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e22679017d846ffb8481b5435dfb88f.json"}}, {"family": "Buisson", "given": "Corinne", "initials": "C"}, {"family": "Bury", "given": "Daniel", "initials": "D", "orcid": "0000-0003-1283-3133", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1f582f4cfb94dc3a2786dab11d8f6eb.json"}}, {"family": "Covaci", "given": "Adrian", "initials": "A", "orcid": "0000-0003-0527-1136", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a7e33db3e224b70838502eb8696c2fd.json"}}, {"family": "Coumoul", "given": "Xavier", "initials": "X"}, {"family": "Debrauwer", "given": "Laurent", "initials": "L"}, {"family": "Del\u00e9p\u00e9e", "given": "Rapha\u00ebl", "initials": "R", "orcid": "0000-0002-9894-1268", "researcher": {"href": "https://publications.scilifelab.se/researcher/26c2e5d9a323415db82b11e0d5cc86d3.json"}}, {"family": "Denys", "given": "Sebastien", "initials": "S"}, {"family": "Dereumeaux", "given": "Cl\u00e9mentine", "initials": "C"}, {"family": "Feuerstein", "given": "Max L", "initials": "ML"}, {"family": "Fillol", "given": "Cl\u00e9mence", "initials": "C"}, {"family": "Gago-Ferrero", "given": "Pablo", "initials": "P", "orcid": "0000-0002-5987-0399", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8da00927802436280b942e26fa425ee.json"}}, {"family": "Garcia", "given": "Patrice", "initials": "P"}, {"family": "Gicquel", "given": "Thomas", "initials": "T", "orcid": "0000-0002-2354-1884", "researcher": {"href": "https://publications.scilifelab.se/researcher/406d7e7c80684e4e9633d0264588d088.json"}}, {"family": "Gil-Solsona", "given": "Ruben", "initials": "R"}, {"family": "Grova", "given": "Nathalie", "initials": "N"}, {"family": "Habchi", "given": "Baninia", "initials": "B", "orcid": "0000-0001-9705-167X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3bc0f14816641d3823a98affd8379cc.json"}}, {"family": "Hernandes", "given": "Vinicius V", "initials": "VV"}, {"family": "Iglesias-Gonz\u00e1lez", "given": "Alba", "initials": "A"}, {"family": "Jamin", "given": "Emilien L", "initials": "EL", "orcid": "0000-0002-4568-9177", "researcher": {"href": "https://publications.scilifelab.se/researcher/18e6892c59da44669cab9378f3f48d4c.json"}}, {"family": "Koch", "given": "Holger M", "initials": "HM", "orcid": "0000-0002-8328-2837", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d858cebb12e4f30b6639191b1c5a5f9.json"}}, {"family": "Lef\u00e8vre-Arbogast", "given": "Sophie", "initials": "S"}, {"family": "Lindh", "given": "Christian", "initials": "C", "orcid": "0000-0001-7435-9890", "researcher": {"href": "https://publications.scilifelab.se/researcher/22cf9d35a123430dae752b434694aaef.json"}}, {"family": "Louyer", "given": "Mari Vorgan", "initials": "MV", "orcid": "0009-0004-3528-8902", "researcher": {"href": "https://publications.scilifelab.se/researcher/57717aae2aa54883bf8944db5b8e990c.json"}}, {"family": "Macheka", "given": "Linda R", "initials": "LR"}, {"family": "Martin", "given": "Jonathan W", "initials": "JW"}, {"family": "Marques", "given": "Montse", "initials": "M"}, {"family": "Mol", "given": "Hans", "initials": "H"}, {"family": "Ndaw", "given": "Sophie", "initials": "S"}, {"family": "Oleko", "given": "Amivi", "initials": "A"}, {"family": "Papazian", "given": "Stefano", "initials": "S"}, {"family": "P\u0159ibylov\u00e1", "given": "Petra", "initials": "P"}, {"family": "Price", "given": "Elliott J", "initials": "EJ"}, {"family": "Schymanski", "given": "Emma L", "initials": "EL", "orcid": "0000-0001-6868-8145", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c430a0ab4994daa9ac8310a48d9da43.json"}}, {"family": "Thiele", "given": "Solveig", "initials": "S", "orcid": "0009-0003-3528-0655", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d9ca015792449f78ea2eb4873e5af40.json"}}, {"family": "Warth", "given": "Benedikt", "initials": "B", "orcid": "0000-0002-6104-0706", "researcher": {"href": "https://publications.scilifelab.se/researcher/51d385ac37f442a5b1fb8fe64ce23dbb.json"}}, {"family": "Zeman", "given": "Florence", "initials": "F"}, {"family": "Blanc", "given": "Etienne", "initials": "E"}, {"family": "Antignac", "given": "Jean Philippe", "initials": "JP"}, {"family": "Le Bizec", "given": "Bruno", "initials": "B", "orcid": "0000-0002-0600-5895", "researcher": {"href": "https://publications.scilifelab.se/researcher/080fcb5697db47cc8990b7b2279cb1a4.json"}}, {"family": "Samson", "given": "Michel", "initials": "M"}], "type": "journal-article", "published": "2026-03-18", "journal": {"title": "Nat Med", "issn": "1078-8956", "issn-l": "1078-8956"}, "abstract": null, "doi": "10.1038/s41591-026-04289-7", "pmid": "41851349", "labels": {"Exposomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41591-026-04289-7"}], "notes": [], "created": "2026-03-24T14:32:25.322Z", "modified": "2026-05-19T13:34:57.928Z"}, {"entity": "publication", "iuid": "8a88693e35b444ce876a3dd11d760a8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a88693e35b444ce876a3dd11d760a8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a88693e35b444ce876a3dd11d760a8e"}}, "title": "FGFR signaling establishes spatial gradients of secretory cell identities along the airway proximal-distal axis.", "authors": [{"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49f693f406b4ba28faf373fa67ee683.json"}}, {"family": "Theelke", "given": "Jonas", "initials": "J", "orcid": "0000-0002-5074-1793", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bfd9c1f49b24c9e8dc5c22bc4288543.json"}}, {"family": "Liontos", "given": "Andreas", "initials": "A"}, {"family": "Firsova", "given": "Alexandra B", "initials": "AB", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications.scilifelab.se/researcher/32fc885aa10d48cebd772ad1470def0c.json"}}, {"family": "Eliot", "given": "Orane", "initials": "O"}, {"family": "Koepke", "given": "Janine", "initials": "J"}, {"family": "Millar-B\u00fcchner", "given": "Pamela", "initials": "P"}, {"family": "Manner\u00e5s-Holm", "given": "Louise", "initials": "L"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "Fysikopoulos", "given": "Athanasios", "initials": "A", "orcid": "0000-0002-8081-0198", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c94301c7ab74979ae2db1c606d9387b.json"}}, {"family": "Kelm", "given": "Antonia", "initials": "A"}, {"family": "Bouloukou", "given": "Eleni", "initials": "E"}, {"family": "Gaengel", "given": "Konstantin", "initials": "K", "orcid": "0000-0002-2682-2833", "researcher": {"href": "https://publications.scilifelab.se/researcher/b405d74174ae47749815a091affb9aea.json"}}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Seeger", "given": "Werner", "initials": "W", "orcid": "0000-0003-1946-0894", "researcher": {"href": "https://publications.scilifelab.se/researcher/36385e53dcd7475ab3f100b63179807b.json"}}, {"family": "Bellusci", "given": "Saverio", "initials": "S"}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/004a4a166cb34d59ba054055658425f6.json"}}], "type": "journal article", "published": "2026-03-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Secretory cells are major structural and functional constituents of the lung airways. Their heterogeneity, spatial organization and specification mechanisms are partially understood. Here, we analyze secretory lung cell-types at single-cell resolution. In the airway epithelium, we find opposing, partially overlapping gene-expression gradients along the proximal-distal airway axis superimposed on a general gene program encoding detoxification. One graded program is elevated proximally and relates to innate immunity, whereas the other is enriched distally, encoding lipid metabolism and antigen presentation. Intermediately positioned cells express moderate levels of both graded programs creating a differentiation continuum towards each end. Lineage tracing analysis during development reveals the sequential establishment of the gradients in common epithelial progenitors postnatally. We show that Fgfr2b regulates the airway patterning by inducing and maintaining high levels of lipid biosynthesis and vesicle trafficking in distal airways and down-regulating innate-immunity genes in vivo and in airway organoids. Our analysis offers a framework for studying epithelial and lung tissue organization to better understand cellular roles in tissue-level pathology.", "doi": "10.1038/s41467-026-70842-0", "pmid": "41851103", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-026-70842-0"}, {"db": "pmc", "key": "PMC13004988"}], "notes": [], "created": "2026-03-23T13:53:27.906Z", "modified": "2026-03-23T13:53:28.385Z"}, {"entity": "publication", "iuid": "483493d2904b4314872a2fb14d09bb93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/483493d2904b4314872a2fb14d09bb93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/483493d2904b4314872a2fb14d09bb93"}}, "title": "The population structure in the Baltic herring reflects natural selection and local adaptation.", "authors": [{"family": "Goodall", "given": "Jake", "initials": "J"}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Andersson", "given": "Anastasia", "initials": "A"}, {"family": "Dahlin", "given": "Iris", "initials": "I"}, {"family": "Ryman", "given": "Nils", "initials": "N"}, {"family": "St\u00e5hl", "given": "Gunnar", "initials": "G"}, {"family": "Wennerstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Laikre", "given": "Linda", "initials": "L"}], "type": "journal article", "published": "2026-03-17", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "123", "issue": "11", "pages": "e2526500123", "issn-l": "0027-8424"}, "abstract": "How species time reproduction and adapt to environmental conditions are key topics in ecology and evolutionary biology. Here, we conducted a high-resolution population genetic analysis of Baltic herring, a subspecies of Atlantic herring (Clupea harengus). Genotypes at >4,500 SNPs were generated from >4,500 spawning individuals, sampled from 150 locations spanning Swedish's eastern coast. Abiotic factors-week of spawning, latitude, temperature, salinity-were used to assess how genetic variation is shaped by temporal, spatial, and environmental gradients. Our results reaffirm strong genetic differentiation between spring- and autumn-spawning ecotypes, despite hybridization suggesting ongoing gene flow between the two ecotypes. We document significant substructuring within the spring-spawning ecotype, delineating three main, previously unidentified, genetic clusters underpinned by adaptative genetic variation associated with latitude, salinity, temperature, and spawning time. Complementary linkage disequilibrium (LD) partitioning showed that adaptive loci-especially those in inversion regions-exhibit strong elevated among-population LD, consistent with divergence maintained by local selection despite ongoing gene flow. Clinal variation in allele frequencies indicated regionally distinct selection pressures, including shifts in allele frequencies at two major supergenes (inversions) and at a suite of genes correlated with abiotic factors. Importantly, rare genetic outlier populations are identified within each geographic region which further illustrates the unexpected fine-grained population structure of Baltic herring and implies a strong homing behavior in this abundant marine fish. Overall, this study demonstrates the capacity for targeted population genetic studies to detect adaptive variation in natural populations, the outcomes of which have direct implications for sustainable fisheries and biodiversity management.", "doi": "10.1073/pnas.2526500123", "pmid": "41802067", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12993978"}], "notes": [], "created": "2026-03-23T14:00:34.838Z", "modified": "2026-03-23T14:00:34.939Z"}, {"entity": "publication", "iuid": "999289be0c1e406bb30bd4b40e7a2f00", "links": {"self": {"href": "https://publications.scilifelab.se/publication/999289be0c1e406bb30bd4b40e7a2f00.json"}, "display": {"href": "https://publications.scilifelab.se/publication/999289be0c1e406bb30bd4b40e7a2f00"}}, "title": "Genomic identification and complete mitochondrial recovery of a Late Holocene porcupine (Erethizon dorsatum) mummy from Yukon permafrost", "authors": [{"family": "Selvatici", "given": "Sofia", "initials": "S"}, {"family": "Jin", "given": "Chenyu", "initials": "C"}, {"family": "Zazula", "given": "Grant", "initials": "G", "orcid": "0000-0001-8436-1783", "researcher": {"href": "https://publications.scilifelab.se/researcher/077650a2501a49eaa9aba0a8b8fc4a56.json"}}, {"family": "Hall", "given": "Elizabeth", "initials": "E", "orcid": "0000-0001-6998-0156", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcfa42cd57c645ba868b8ab621a1be14.json"}}, {"family": "Hewitson", "given": "Susan", "initials": "S", "orcid": "0000-0003-0091-012X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0a989b12c524e859eb20fdc38d2c111.json"}}, {"family": "Moots", "given": "Hannah M", "initials": "HM", "orcid": "0000-0002-6637-6321", "researcher": {"href": "https://publications.scilifelab.se/researcher/5105354f578c480ba144061ffbb49bf5.json"}}, {"family": "Sharif", "given": "Bilal", "initials": "B"}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}}, {"family": "Parducci", "given": "Laura", "initials": "L", "orcid": "0000-0003-1956-4757", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed4c737e2c7c4266b598a89aa2116a91.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "D\u00edez-del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "Oteo-Garc\u00eda", "given": "Gonzalo", "initials": "G", "orcid": "0000-0002-0957-4014", "researcher": {"href": "https://publications.scilifelab.se/researcher/62bbfad753a943ea94eb9a0384713a17.json"}}], "type": "journal-article", "published": "2026-03-17", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "We identified a 3000-year-old specimen from the Traditional Territory of the Tr'ond\u00ebk Hw\u00ebch'in in central Yukon Territory, Canada as the first known mummified remains of an ancient North American porcupine (Erethizon dorsatum), known as \"Ts'ey\" in the H\u00e4n language, using genetic analysis and metagenomic validation. Our analysis of the sample yielded the first-ever complete ancient mitochondrial genome for (E. dorsatum) and only the second full mitogenome for the species. Its Holocene age is considerably younger than the Pleistocene megafauna typically recovered in the Yukon permafrost, demonstrating the potential for these deposits to preserve specimens from interglacial periods. Crucially, this finding confirms the presence of porcupines in the region 3000 years ago, in line with the hypothesis that this species only dispersed into Yukon and Alaska following the establishment of boreal forests after the Last Glacial Period.", "doi": "10.1038/s41598-026-44540-2", "pmid": "41845022", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12996357"}, {"db": "pii", "key": "10.1038/s41598-026-44540-2"}], "notes": [], "created": "2026-03-23T13:18:35.892Z", "modified": "2026-03-24T09:12:30.461Z"}, {"entity": "publication", "iuid": "49030089ac5e463a815a0459fdcfe9a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49030089ac5e463a815a0459fdcfe9a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49030089ac5e463a815a0459fdcfe9a2"}}, "title": "Paralog-aware assembly and filtering strategies reveal minimal nucleotide variation on the macro germline-restricted chromosome of the zebra finch.", "authors": [{"family": "Chen", "given": "Augustin", "initials": "A", "orcid": "0000-0002-2016-3048", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db30961a7d74af8992748220415b643.json"}}, {"family": "Ruiz-Ruano", "given": "Francisco J", "initials": "FJ", "orcid": "0000-0002-5391-301X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37ccedb49884e27aeffed3b49085ddf.json"}}, {"family": "Contreras-L\u00f3pez", "given": "Orlando", "initials": "O", "orcid": "0000-0002-4048-6637", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b2d9f2bfc8843d4a2f75eae2cbe76a4.json"}}, {"family": "Fouch\u00e9", "given": "Simone", "initials": "S", "orcid": "0000-0003-0601-6073", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b5335a456624aaeac268a1489c00b1f.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-2411-4454", "researcher": {"href": "https://publications.scilifelab.se/researcher/af91cebf5fa04abb9656aaf9123ad53b.json"}}, {"family": "Pei", "given": "Yifan", "initials": "Y", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}], "type": "journal article", "published": "2026-03-16", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "issn-l": "0018-067X"}, "abstract": "The germline-restricted chromosome (GRC) of passerines is a remarkable tissue-specific chromosome that accumulated paralogs of genes from the regular \"A chromosomes\" over millions of years, often amplified into dozens of gene copies. In addition to its repetitive content, typically uniparental inheritance, and lack of recombination, the GRC resembles non-recombining sex chromosomes and some B chromosomes, for all of which assembly and single-nucleotide polymorphisms (SNPs) calling are difficult. Here, we first show that much of the Australian zebra finch macro-GRC can be assembled using accurate long reads. We then describe a paralog-aware Snakemake pipeline, ParaVar, to map short reads from the GRC to retrieve GRC regions suitable for haplotype-based analysis. ParaVar reliably calls hundreds of SNPs across the GRC, thereby providing an estimate of nucleotide diversity on the highly repetitive zebra finch macro-GRC. Our results show significantly lower nucleotide diversity (20- to 50-fold lower) on the GRC compared to the mitogenome and autosomes, and a strong phylogenetic discordance between the GRC and the mitochondrial genome. Beyond the contribution of background selection, our results suggest that a single GRC haplotype recently spread through the populations while jumping across matrilines via occasional paternal inheritance. We anticipate that our paralog-aware pipeline will be useful for SNP calling and population genetics analyses of repetitive GRCs, sex chromosomes, and B chromosomes.", "doi": "10.1038/s41437-026-00830-z", "pmid": "41840191", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Short read": "Service", "NGI Other": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41437-026-00830-z"}], "notes": [], "created": "2026-03-23T15:23:33.935Z", "modified": "2026-03-23T15:23:34.639Z"}, {"entity": "publication", "iuid": "654a81a53ea648719ebdd68ff020c8dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/654a81a53ea648719ebdd68ff020c8dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/654a81a53ea648719ebdd68ff020c8dc"}}, "title": "Midostaurin response in AML is shaped by a progenitor-like cell state selectively targeted by SMAC mimetics.", "authors": [{"family": "Struyf", "given": "Nona", "initials": "N"}, {"family": "Gezelius", "given": "Henrik", "initials": "H"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Barizza", "given": "Chiara", "initials": "C"}, {"family": "Ploeger", "given": "Hidde", "initials": "H"}, {"family": "Rico Pizarro", "given": "Lucia", "initials": "L"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M"}, {"family": "Mermelekas", "given": "Georgios", "initials": "G"}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": "Bengtz\u00e9n", "given": "Sofia", "initials": "S"}, {"family": "Hamberg Levedahl", "given": "Kerstin", "initials": "K"}, {"family": "Jafari", "given": "Rozbeh", "initials": "R"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Erkers", "given": "Tom", "initials": "T"}], "type": "journal article", "published": "2026-03-11", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "10", "issue": "1", "issn-l": null}, "abstract": "FLT3-mutated acute myeloid leukemia (AML) remains difficult to treat due to frequent resistance to FLT3 inhibitors like midostaurin. In this study, we observed a progenitor-like CD38+CD45RA+ leukemic cell population that may be associated with midostaurin resistance. Midostaurin-resistant cells display disrupted membrane architecture and a shift in signaling from STAT5 to PI3K/AKT, favoring survival over apoptosis. Functional drug testing was consistent with clinical response to midostaurin, and together with multi-omic profiling, including single-cell and proteomic analyses, indicated the presence and relevance of this resistant phenotype. Drug combination screening revealed that co-targeting with SMAC mimetics restores apoptotic competence and selectively depletes the resistant population when combined with midostaurin. In contrast, venetoclax combinations preferentially affected CD34hi cells, underscoring distinct subpopulation vulnerabilities. These findings may point to a biologically relevant mechanism underlying midostaurin resistance.", "doi": "10.1038/s41698-026-01363-8", "pmid": "41813823", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12996285"}, {"db": "pii", "key": "10.1038/s41698-026-01363-8"}], "notes": [], "created": "2026-05-27T11:37:54.401Z", "modified": "2026-05-27T11:37:54.406Z"}, {"entity": "publication", "iuid": "e5ec787139724ab0bcd41b3b3b928147", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5ec787139724ab0bcd41b3b3b928147.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5ec787139724ab0bcd41b3b3b928147"}}, "title": "Persistent interferon signaling causes sensory neuron plasticity and pain before and during arthritis.", "authors": [{"family": "Su", "given": "Jie", "initials": "J", "orcid": "0000-0001-9828-9794", "researcher": {"href": "https://publications.scilifelab.se/researcher/228f25d52aef47d9b5b0d1000fed5ea7.json"}}, {"family": "Zhang", "given": "Ming-Dong", "initials": "MD", "orcid": "0000-0002-6348-1994", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1585272a1848508d8f2395ace61332.json"}}, {"family": "Kupari", "given": "Jussi", "initials": "J"}, {"family": "Kwak", "given": "Dongoh", "initials": "D"}, {"family": "Picton", "given": "Laurence", "initials": "L"}, {"family": "Xu", "given": "Bingze", "initials": "B"}, {"family": "do Nascimento", "given": "Leandro Flores", "initials": "LF"}, {"family": "Hu", "given": "Yizhou", "initials": "Y", "orcid": "0000-0002-2635-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b75010a59c243279eaf9ca7af75315b.json"}}, {"family": "Gonzalez", "given": "Alejandro", "initials": "A", "orcid": "0000-0001-7513-2516", "researcher": {"href": "https://publications.scilifelab.se/researcher/df94b05dc87c4d5f9e9939170f4d001f.json"}}, {"family": "Usoskin", "given": "Dmitry", "initials": "D", "orcid": "0000-0001-9122-6387", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4848f28ec474a71b8240ff6ab553444.json"}}, {"family": "Xu", "given": "Zhongwei", "initials": "Z", "orcid": "0000-0001-5178-3437", "researcher": {"href": "https://publications.scilifelab.se/researcher/f056000b3af842bda8cdd411da7d44ad.json"}}, {"family": "Szczot", "given": "Marcin", "initials": "M", "orcid": "0000-0002-3902-059X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4fef830b2914f37b100c433fbdd4fd0.json"}}, {"family": "El Manira", "given": "Abdeljabbar", "initials": "A", "orcid": "0000-0001-5920-9384", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c6e1ed8fbb547b1844b979220d8514a.json"}}, {"family": "Holmdahl", "given": "Rikard", "initials": "R", "orcid": "0000-0002-4969-2576", "researcher": {"href": "https://publications.scilifelab.se/researcher/49e60d22dd1a4dd1a4ca5a50d9fc4fc7.json"}}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}], "type": "journal article", "published": "2026-03-10", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256"}, "abstract": "Although inflammatory processes in rheumatoid arthritis have been described, mechanisms driving pain are poorly defined. Here, we used a multitude of approaches to uncover the neural basis and causes of inflammatory pain. We show in mice with cartilage autoantibody-induced arthritis that early immune activation and a cytokine storm were mainly driven by vascular cells and monocytes/macrophages in the dorsal root ganglion. However, persistently elevated interferons and receptor activation of the MNK1/MNK2-eIF4E signaling pathway at all disease phases caused sensory-motor dysfunction and pain by inducing hyperexcitability and sensitization of a GFRA3+ C-fiber subtype of joint-innervating sensory neurons. Signaling pathway inhibition in vivo reversed pain and restored limb function. Like mice, human sensory neurons expressed interferon receptors, and type 1 interferons and signaling were increased only in individuals with painful rheumatoid arthritis. The finding that joint pain before and during arthritis is caused by a defined cytokine and signaling pathway holds promise for targeted therapies for pain relief in arthritis.", "doi": "10.1038/s41593-026-02234-y", "pmid": "41807847", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-026-02234-y"}], "notes": [], "created": "2026-03-23T15:25:03.672Z", "modified": "2026-03-23T15:25:04.053Z"}, {"entity": "publication", "iuid": "0e1dde47e7304f09b029297f6c8335fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e1dde47e7304f09b029297f6c8335fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e1dde47e7304f09b029297f6c8335fb"}}, "title": "Whole genomes reveal subpopulations and isolation-by-distance patterns in the Norwegian lemming.", "authors": [{"family": "Feinauer", "given": "Isabelle Sofie", "initials": "IS", "orcid": "0009-0004-4615-0810", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d95245a50e408a9643a18b7c0fc3d2.json"}}, {"family": "Ravasini", "given": "Francesco", "initials": "F"}, {"family": "Lagerholm", "given": "Vendela Kempe", "initials": "VK"}, {"family": "M\u00e5sviken", "given": "Johannes", "initials": "J", "orcid": "0000-0003-2660-7081", "researcher": {"href": "https://publications.scilifelab.se/researcher/b060865f580a44f29d46bf1bb6030f1f.json"}}, {"family": "Olsen", "given": "Remi-Andre", "initials": "RA", "orcid": "0009-0002-8357-5186", "researcher": {"href": "https://publications.scilifelab.se/researcher/5419b796720a47c8aa7a26ca663a96bd.json"}}, {"family": "Soler", "given": "Lucile", "initials": "L", "orcid": "0000-0002-0121-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/f701059f90fe4c7c9b969079e74aac57.json"}}, {"family": "Proux-Wera", "given": "Estelle", "initials": "E", "orcid": "0000-0003-3752-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9257ccdfc6484cd9a95f9b2f17f9a8d1.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Lantz", "given": "Henrik", "initials": "H", "orcid": "0000-0003-2419-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/85fa15d934214e00bb7818b865c4d754.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Ehrich", "given": "Dorothee", "initials": "D", "orcid": "0000-0002-3028-9488", "researcher": {"href": "https://publications.scilifelab.se/researcher/c056bc462f8e433ba76bc65bb308df9b.json"}}, {"family": "Ims", "given": "Rolf A", "initials": "RA"}, {"family": "Henttonen", "given": "Heikki", "initials": "H"}, {"family": "Eide", "given": "Nina E", "initials": "NE"}, {"family": "Flagstad", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K", "orcid": "0000-0002-9707-5206", "researcher": {"href": "https://publications.scilifelab.se/researcher/40450a7e8cda45ba8292b9a677b3fb29.json"}}, {"family": "Angerbj\u00f6rn", "given": "Anders", "initials": "A"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2026-03-06", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "24", "issue": "1", "issn-l": "1741-7007"}, "abstract": "The Norwegian lemming (Lemmus lemmus) is a small rodent endemic to the Fennoscandian alpine and arctic tundra. The species is known for cyclic population outbreaks and mass movements during peak years. Previous research based on microsatellites revealed high genetic variation but a weak population structure in the Norwegian lemming.\n\nIn this study, we revisit the population structure of the species using genome-wide data. To do this, we generated a high-quality de novo reference genome for Lemmus lemmus, and resequenced genomes to 2.5-5 \u00d7 coverage, from 86 lemmings sampled across the species' entire geographic distribution. Our results reveal that the population is geographically structured into distinct subpopulations, with an overall pattern characterised by isolation-by-distance among subpopulations. Furthermore, our results are consistent with earlier work suggesting that the species survived the last ice age within a northern refugium.\n\nTogether, these findings provide a genome-wide perspective on today's population structure of the Norwegian lemming. In addition, we provide a de novo reference genome, which we believe will be a valuable resource to the research community.", "doi": "10.1186/s12915-026-02568-w", "pmid": "41787358", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13064042"}, {"db": "pii", "key": "10.1186/s12915-026-02568-w"}], "notes": [], "created": "2026-03-23T13:20:06.509Z", "modified": "2026-06-01T08:42:50.558Z"}, {"entity": "publication", "iuid": "56a35d53dd074855a03836ab41cdc335", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56a35d53dd074855a03836ab41cdc335.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56a35d53dd074855a03836ab41cdc335"}}, "title": "Polycomb repression works without Siesta, the Drosophila ortholog of mammalian PCGF3.", "authors": [{"family": "Kahn", "given": "Tatyana G", "initials": "TG", "orcid": "0000-0001-6109-6243", "researcher": {"href": "https://publications.scilifelab.se/researcher/2981d13fc748402cad966852e9d00395.json"}}, {"family": "Garrido", "given": "Andres", "initials": "A", "orcid": "0009-0000-7738-4397", "researcher": {"href": "https://publications.scilifelab.se/researcher/68346f49e1ec4a9f813fc916f7e7fa5d.json"}}, {"family": "Yushkova", "given": "Anastasiya", "initials": "A", "orcid": "0000-0002-9037-6866", "researcher": {"href": "https://publications.scilifelab.se/researcher/93639e0c8c504000a5a2bdf459a149a1.json"}}, {"family": "Kim", "given": "Maria", "initials": "M"}, {"family": "Glotov", "given": "Alexander", "initials": "A"}, {"family": "Sreekumar", "given": "Sweda", "initials": "S"}, {"family": "Larsson", "given": "Jan", "initials": "J", "orcid": "0000-0003-4373-6790", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d6f8e41628d4534879edaf229575dec.json"}}, {"family": "Schwartz", "given": "Yuri B", "initials": "YB", "orcid": "0000-0003-4790-3920", "researcher": {"href": "https://publications.scilifelab.se/researcher/2751a236629d4b8bb9fff42cad6ff614.json"}}], "type": "journal article", "published": "2026-03-06", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "12", "issue": "10", "pages": "eaec0733", "issn-l": "2375-2548"}, "abstract": "Polycomb group proteins mediate epigenetic repression via multisubunit complexes, including canonical Polycomb Repressive Complex 1 (PRC1), which monoubiquitylates histone H2A and binds histone H3 trimethylated at lysine-27 (H3K27me3). The RING1 subunit of PRC1, critical for H2A ubiquitylation, forms other complexes. These variant RING1 complexes also ubiquitylate H2A but cannot bind H3K27me3, and their role in epigenetic repression is debated. Using Drosophila genetics, we found that canonical PRC1 and variant RING1 complexes ubiquitylate H2A at distinct genomic regions. We established that the Drosophila PCGF protein specific for variant RING1 complexes, which we named Siesta, is not required for epigenetic repression of developmental genes but controls larval locomotion independently of H2A ubiquitylation. Leveraging a massively parallel transgenic approach, we demonstrated that H2A ubiquitylation has minimal impact on transcriptional repression. Our findings imply that Siesta-RING1 complexes operate outside the Polycomb regulatory system and that the popular PRC1 classification will benefit from revision.", "doi": "10.1126/sciadv.aec0733", "pmid": "41790891", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12965321"}], "notes": [], "created": "2026-06-01T11:10:51.338Z", "modified": "2026-06-01T11:10:51.612Z"}, {"entity": "publication", "iuid": "4a7100c23e144b7abdf8d58ddb80b6c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a7100c23e144b7abdf8d58ddb80b6c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a7100c23e144b7abdf8d58ddb80b6c6"}}, "title": "Above-Filter Digestion Proteomics Reveals Drug Targets and Localizes Ligand Binding Site.", "authors": [{"family": "Sokolova", "given": "Bohdana", "initials": "B", "orcid": "0000-0003-3751-7129", "researcher": {"href": "https://publications.scilifelab.se/researcher/6276043c6670459785d175983f625167.json"}}, {"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications.scilifelab.se/researcher/b85179acfa7e4916ad40ae478d6dcc0a.json"}}, {"family": "Jafari", "given": "Maryam", "initials": "M"}, {"family": "Lyu", "given": "Hezheng", "initials": "H"}, {"family": "Lovera", "given": "Silvia", "initials": "S"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "Saei", "given": "Amir Ata", "initials": "AA"}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "journal article", "published": "2026-03-06", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "25", "issue": "3", "pages": "1556-1570", "issn-l": "1535-3893"}, "abstract": "Identifying how drugs interact with proteins is fundamental to understanding their therapeutic effects and side effects. While numerous chemical proteomics methods exist for determining protein targets of drugs, each exhibits \"blind spots,\" necessitating complementary approaches. We introduce Above-Filter Digestion Proteomics (AFDIP), which monitors trypsin digestion rates that decrease at ligand-binding sites, while potentially increasing elsewhere. Molecular dynamics simulations showed that these changes relate to backbone flexibility. Using AFDIP, we identified targets of various drugs and metabolites, allowing two-dimensional analysis with the drug concentration as the second dimension. The method identifies binding sites within \u226410 \u00c5 of crystallography-determined locations with improved resolution (\u22645 \u00c5) for larger proteins. Compared with existing proteolysis approaches, AFDIP offers simpler sample preparation, deeper proteome analysis, and broader sequence coverage. AFDIP addresses the blind spots of current techniques and provides structural insights, enhancing the chemical proteomics toolkit.", "doi": "10.1021/acs.jproteome.5c00927", "pmid": "41653152", "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12973292"}], "notes": [], "created": "2026-05-25T19:27:19.747Z", "modified": "2026-05-25T19:27:20.312Z"}, {"entity": "publication", "iuid": "b31162b460c7480c87a7be42d41b600a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b31162b460c7480c87a7be42d41b600a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b31162b460c7480c87a7be42d41b600a"}}, "title": "The HUNT study identifies host genetic factors reproducibly associated with human gut microbiota composition", "authors": [{"family": "Moksnes", "given": "Marta Riise", "initials": "MR", "orcid": "0000-0002-2690-5153", "researcher": {"href": "https://publications.scilifelab.se/researcher/15fd5ce3d43a4b76a7a7e710e8724a6f.json"}}, {"family": "Coward", "given": "Eivind", "initials": "E", "orcid": "0009-0008-1323-3555", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a4792db14b645b9b5134243f9ca7b60.json"}}, {"family": "Nethander", "given": "Maria", "initials": "M", "orcid": "0000-0003-3688-906X", "researcher": {"href": "https://publications.scilifelab.se/researcher/53d61951f51c4d40bef24672866382cb.json"}}, {"family": "Dekkers", "given": "Koen", "initials": "K", "orcid": "0000-0002-4074-7235", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee8d56ef781e42d5b6f21b551054a3e7.json"}}, {"family": "Grahnemo", "given": "Louise", "initials": "L", "orcid": "0000-0001-5276-6612", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb1ac8fe74954a5db43e8e6538cf8235.json"}}, {"family": "T\u00f6rnqvist", "given": "Anna E", "initials": "AE"}, {"family": "Li", "given": "Lei", "initials": "L"}, {"family": "Lundmark", "given": "Per", "initials": "P", "orcid": "0009-0006-2334-8802", "researcher": {"href": "https://publications.scilifelab.se/researcher/f30b1a2e60d646c4a0cc0be06ffe77dd.json"}}, {"family": "Pertiwi", "given": "Kamalita", "initials": "K", "orcid": "0000-0003-2861-9051", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9cb279b53204e51b202134c82cf680f.json"}}, {"family": "Baldanzi", "given": "Gabriel", "initials": "G", "orcid": "0000-0003-3962-3953", "researcher": {"href": "https://publications.scilifelab.se/researcher/577652ffb15442e1a47a9aaffc3b52e7.json"}}, {"family": "Mjelle", "given": "Robin", "initials": "R"}, {"family": "Moll", "given": "Janne Marie", "initials": "JM", "orcid": "0000-0002-3514-4528", "researcher": {"href": "https://publications.scilifelab.se/researcher/52e482fb976e4bb3a212d98b981c9f2f.json"}}, {"family": "Eklund", "given": "Aron Charles", "initials": "AC", "orcid": "0000-0003-0861-1001", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1b0f6b48de45f7916e14d6a4defb09.json"}}, {"family": "Nielsen", "given": "Henrik Bj\u00f8rn", "initials": "HB", "orcid": "0000-0003-2281-5713", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1d5f2e0565a46bcbccfc973eec9e838.json"}}, {"family": "Svensson", "given": "Johan", "initials": "J", "orcid": "0000-0002-4487-6405", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdbca5fe77124646b51e9c55dae4d361.json"}}, {"family": "Langhammer", "given": "Arnulf", "initials": "A", "orcid": "0000-0001-5296-6673", "researcher": {"href": "https://publications.scilifelab.se/researcher/755b4b39d8054f2ea3e28476a7b0ae39.json"}}, {"family": "Giske\u00f8deg\u00e5rd", "given": "Guro F", "initials": "GF", "orcid": "0000-0003-2157-8824", "researcher": {"href": "https://publications.scilifelab.se/researcher/57d6962d8112403fb823764ce0a0d6c6.json"}}, {"family": "Brumpton", "given": "Ben", "initials": "B", "orcid": "0000-0002-3058-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/da9d23aaf1dc4d18a0a13e4847ea9955.json"}}, {"family": "Hjort", "given": "Rebecka", "initials": "R"}, {"family": "Ness-Jensen", "given": "Eivind", "initials": "E", "orcid": "0000-0001-6005-0729", "researcher": {"href": "https://publications.scilifelab.se/researcher/d619713fc5764a5e9b88c7c012cf0cf1.json"}}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-8618-9152", "researcher": {"href": "https://publications.scilifelab.se/researcher/b40c03613a3a46368ed855fc95b79e31.json"}}, {"family": "Pelaseyed", "given": "Thaher", "initials": "T", "orcid": "0000-0002-6434-3913", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dc0aa3d9762420caa7efaaa19c1174b.json"}}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K", "orcid": "0000-0003-2815-1217", "researcher": {"href": "https://publications.scilifelab.se/researcher/eff63868e95240f695d47e871e31947f.json"}}, {"family": "Orho-Melander", "given": "Marju", "initials": "M", "orcid": "0000-0002-3578-2503", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e54fbe6f0fc4eed93108b382e1b2952.json"}}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Ohlsson", "given": "Claes", "initials": "C", "orcid": "0000-0002-9633-2805", "researcher": {"href": "https://publications.scilifelab.se/researcher/995dac358caa4a169fc889b7a3eef44a.json"}}], "type": "journal-article", "published": "2026-03-00", "journal": {"title": "Nat Genet", "issn": "1061-4036", "volume": "58", "issue": "3", "pages": "530-539", "issn-l": "1061-4036"}, "abstract": "The gut microbiota is associated with human health and disease. Here we conducted a genome-wide association study of host genetic factors influencing gut microbiota composition in 12,652 individuals from the Tr\u00f8ndelag Health Study (HUNT), with replication in Nordic cohorts (n = 16,017-21,976). We identified 12 reproducible SNP-species associations across six genomic loci, including known (LCT, ABO) and novel (HLA-DQB1, MUC12, SLC37A2, FUT2) regions. Additionally, we detected genetic signals associated with gut microbiota functional modules at three loci (LCT, ABO, FUT2). Follow-up analyses suggest that these host-microbiota associations are linked to the pathogenesis of celiac disease and hemorrhoidal disease. Mendelian randomization analyses provided evidence supporting a causal effect of body mass index on gut microbiota composition. These findings highlight the interplay between host genetics and gut microbiota for human health and disease.", "doi": "10.1038/s41588-026-02502-4", "pmid": "41688637", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12987729"}, {"db": "pii", "key": "10.1038/s41588-026-02502-4"}], "notes": [], "created": "2026-03-19T16:36:31.375Z", "modified": "2026-03-24T09:08:07.330Z"}, {"entity": "publication", "iuid": "79685133481d424091f6bbe60bed024e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79685133481d424091f6bbe60bed024e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79685133481d424091f6bbe60bed024e"}}, "title": "Resource Availability Modulates Gene Expression Across Life Stages in a Migratory Butterfly.", "authors": [{"family": "Shipilina", "given": "D", "initials": "D", "orcid": "0000-0002-1145-9226", "researcher": {"href": "https://publications.scilifelab.se/researcher/758a7bdbc6654826ab7f06cf3938b5c3.json"}}, {"family": "H\u00f6\u00f6k", "given": "L", "initials": "L"}, {"family": "N\u00e4svall", "given": "K", "initials": "K"}, {"family": "Talla", "given": "V", "initials": "V"}, {"family": "Palah\u00ed", "given": "A", "initials": "A"}, {"family": "Parkes", "given": "E", "initials": "E"}, {"family": "Vila", "given": "R", "initials": "R", "orcid": "0000-0002-2447-4388", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f9f7ce050d463bb9a67d6970b9428a.json"}}, {"family": "Talavera", "given": "G", "initials": "G", "orcid": "0000-0003-1112-1345", "researcher": {"href": "https://publications.scilifelab.se/researcher/1081486b2353478b8dba3388e819822b.json"}}, {"family": "Backstr\u00f6m", "given": "N", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "35", "issue": "5", "pages": "e70293", "issn-l": "0962-1083"}, "abstract": "Natural populations are in constant need of balancing resource allocation to compensate for seasonal environmental variation. In many insects, a well-established trade-off between migration and reproduction exists. While this trade-off has been characterised phenotypically for decades, the underlying regulatory pathways are poorly understood. Here, we examined how resource-related environmental cues shape transcription across development in the long-distance migrant butterfly Vanessa cardui. In a multi-cue, developmental stage-specific design, adult females were exposed to host-plant presence or absence, while larvae experienced food limitation or crowding. Adult exposure to host plants was associated with differential expression in ecdysteroid and juvenile-hormone pathways, consistent with endocrine regulation of reproductive readiness and predictions of the oogenesis-flight syndrome. Larval resource limitation altered developmental and metabolic pathways, suggesting molecular predispositions and potential carry-over effects to adult traits. Across all contrasts, metabolism emerged as a shared axis linking responses across life stages. Together, our results show that resource-driven cues leave both stage-specific and general transcriptional signatures that connect environmental context with the molecular basis of migratory behaviour.", "doi": "10.1111/mec.70293", "pmid": "41797265", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12968515"}], "notes": [], "created": "2026-03-23T13:21:43.409Z", "modified": "2026-03-23T13:21:43.572Z"}, {"entity": "publication", "iuid": "9483d68accf74a18a06c559536d0ae1d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9483d68accf74a18a06c559536d0ae1d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9483d68accf74a18a06c559536d0ae1d"}}, "title": "Optimizing T cell responses of targeted peptide antigen delivery by modulating antigen processing through amino acid exchange.", "authors": [{"family": "Laur\u00e9n", "given": "Ida", "initials": "I"}, {"family": "Kostakis", "given": "Alexandros", "initials": "A"}, {"family": "Lord", "given": "Martin", "initials": "M"}, {"family": "Bj\u00f6rklund", "given": "Elvira", "initials": "E"}, {"family": "Wang", "given": "Xinyang", "initials": "X"}, {"family": "Tari", "given": "Paria Samadi", "initials": "PS"}, {"family": "Veerman", "given": "Rosanne E", "initials": "RE"}, {"family": "Saleh", "given": "Aljona", "initials": "A"}, {"family": "Mebrahtu", "given": "Aman", "initials": "A"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "D\u00f6nnes", "given": "Pierre", "initials": "P"}, {"family": "Andersson", "given": "Oskar", "initials": "O"}, {"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "Juriga", "given": "David", "initials": "D"}, {"family": "Hansson", "given": "Per", "initials": "P"}, {"family": "Mangsbo", "given": "Sara", "initials": "S"}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "International Journal of Biological Macromolecules", "issn": "1879-0003", "volume": "352", "pages": "151135", "issn-l": "0141-8130"}, "abstract": "Antibody-drug conjugates have demonstrated enhanced efficacy and reduced toxicity by targeted delivery of toxic payloads, yet they can also be used to deliver non-toxic payloads (peptides and oligonucleotides) tailored for disease-specific needs. We have previously developed an adaptable drug conjugate strategy using a high-affinity single-chain variable fragment specific for a short unstructured synthetic peptide tag (pTag). When this fragment is fused to an antibody structure, payload loading can be performed by a simple mixing step provided that the pTag is part of the payload. To assess the impact on conjugate stability and biological responses, we evaluated variants of the pTag by introducing amino acid changes at a central position for affinity binding. In a competition ELISA, a 2.4-fold reduction in IC50 was noted for a non-conservative amino acid alteration (pTagK8L), whereas a conservative amino acid substitution (pTagK8H) resulted in a 1.3-fold decrease compared to the pTag. The non-conservative amino acid change (pTagK8L) negatively influenced the stability of the conjugate, illustrated in a hydrogel model. Additionally, the pTagK8L alteration led to increased CD8+ T cell proliferation and a slight decrease in CD4+ T cell proliferation in vitro. This was irrespective of whether formulated with the bispecific antibody or not. In vivo, the data displayed that the pTag led to significantly higher T cell expansion than the pTagK8L, suggesting that lower affinity may impair immune activation and that conjugation stability is key to achieving the desired targeted delivery capacity.", "doi": "10.1016/j.ijbiomac.2026.151135", "pmid": "41765300", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "S0141-8130(26)01061-5"}], "notes": [], "created": "2026-05-14T20:28:19.841Z", "modified": "2026-05-14T20:28:19.844Z"}, {"entity": "publication", "iuid": "26ae168bcaae4157b24204c508a969d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26ae168bcaae4157b24204c508a969d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26ae168bcaae4157b24204c508a969d8"}}, "title": "Mycelial biomass growth stage at death determines fungal necromass decay dynamics", "authors": [{"family": "Maillard", "given": "Fran\u00e7ois", "initials": "F", "orcid": "0000-0002-2144-5629", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04148cdb36f4b949f2d3209b73d254f.json"}}, {"family": "Lopes Ramos", "given": "Danny", "initials": "D"}, {"family": "Zhang", "given": "Bowen", "initials": "B", "orcid": "0000-0002-3565-8297", "researcher": {"href": "https://publications.scilifelab.se/researcher/a779fcdb12214860a094b7c442d79f03.json"}}, {"family": "Ahlawat", "given": "Ashish", "initials": "A", "orcid": "0000-0003-1671-9864", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7a14ee15edd4ad99fb7ff82b6e28c05.json"}}, {"family": "Gill", "given": "Allison L", "initials": "AL"}, {"family": "Troein", "given": "Carl", "initials": "C", "orcid": "0000-0001-9729-8891", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fd82b431115459289901d245cdb9061.json"}}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M", "orcid": "0000-0002-0903-6662", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db0f81a369741b0847c6f79746d82aa.json"}}, {"family": "Sparrman", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4442-6367", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d27dbd2f014795b1f7aa164d34bada.json"}}, {"family": "Persson", "given": "Per", "initials": "P", "orcid": "0000-0001-9172-3068", "researcher": {"href": "https://publications.scilifelab.se/researcher/edffc6f9df60444a9480380c68e7d202.json"}}, {"family": "Tunlid", "given": "Anders", "initials": "A"}], "type": "journal-article", "published": "2026-03-00", "journal": {"title": "Soil Biology and Biochemistry", "issn": "0038-0717", "volume": "214", "pages": "110079", "issn-l": null}, "abstract": null, "doi": "10.1016/j.soilbio.2025.110079", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-01-08T13:24:44.674Z", "modified": "2026-03-24T09:08:21.656Z"}, {"entity": "publication", "iuid": "1021326661cc476399928b055a37a4e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1021326661cc476399928b055a37a4e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1021326661cc476399928b055a37a4e8"}}, "title": "Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation.", "authors": [{"family": "Dekkers", "given": "Koen F", "initials": "KF", "orcid": "0000-0002-4074-7235", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee8d56ef781e42d5b6f21b551054a3e7.json"}}, {"family": "Pertiwi", "given": "Kamalita", "initials": "K", "orcid": "0000-0003-2861-9051", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9cb279b53204e51b202134c82cf680f.json"}}, {"family": "Baldanzi", "given": "Gabriel", "initials": "G", "orcid": "0000-0003-3962-3953", "researcher": {"href": "https://publications.scilifelab.se/researcher/577652ffb15442e1a47a9aaffc3b52e7.json"}}, {"family": "Lundmark", "given": "Per", "initials": "P", "orcid": "0009-0006-2334-8802", "researcher": {"href": "https://publications.scilifelab.se/researcher/f30b1a2e60d646c4a0cc0be06ffe77dd.json"}}, {"family": "Hammar", "given": "Ulf", "initials": "U"}, {"family": "Moksnes", "given": "Marta Riise", "initials": "MR", "orcid": "0000-0002-2690-5153", "researcher": {"href": "https://publications.scilifelab.se/researcher/15fd5ce3d43a4b76a7a7e710e8724a6f.json"}}, {"family": "Coward", "given": "Eivind", "initials": "E", "orcid": "0009-0008-1323-3555", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a4792db14b645b9b5134243f9ca7b60.json"}}, {"family": "Nethander", "given": "Maria", "initials": "M", "orcid": "0000-0003-3688-906X", "researcher": {"href": "https://publications.scilifelab.se/researcher/53d61951f51c4d40bef24672866382cb.json"}}, {"family": "Salih", "given": "Ghassan Ali", "initials": "GA", "orcid": "0009-0003-5938-8222", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6d97b18c7cc44dcbc9aed652c6f7c46.json"}}, {"family": "Miari", "given": "Mariam", "initials": "M"}, {"family": "Nguyen", "given": "Diem", "initials": "D", "orcid": "0000-0002-9680-5772", "researcher": {"href": "https://publications.scilifelab.se/researcher/d78958133e474831ac76dacc36f68cbb.json"}}, {"family": "Sayols-Baixeras", "given": "Sergi", "initials": "S"}, {"family": "Eklund", "given": "Aron C", "initials": "AC", "orcid": "0000-0003-0861-1001", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1b0f6b48de45f7916e14d6a4defb09.json"}}, {"family": "Holm", "given": "Jacob Bak", "initials": "JB", "orcid": "0000-0003-1756-0875", "researcher": {"href": "https://publications.scilifelab.se/researcher/359fa6a18dc549a8852dd3990ccde1f1.json"}}, {"family": "Nielsen", "given": "H Bj\u00f8rn", "initials": "HB", "orcid": "0000-0003-2281-5713", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1d5f2e0565a46bcbccfc973eec9e838.json"}}, {"family": "Volpiano", "given": "Camila Gazolla", "initials": "CG"}, {"family": "M\u00e9ric", "given": "Guillaume", "initials": "G", "orcid": "0000-0001-6288-9958", "researcher": {"href": "https://publications.scilifelab.se/researcher/229f8c463d1a4eef945c2b62b77977ab.json"}}, {"family": "Thangam", "given": "Manonanthini", "initials": "M", "orcid": "0000-0002-7164-6525", "researcher": {"href": "https://publications.scilifelab.se/researcher/d09c26b1d20c4539b46824ee62c69ded.json"}}, {"family": "Hakaste", "given": "Liisa", "initials": "L"}, {"family": "Tuomi", "given": "Tiinamaija", "initials": "T"}, {"family": "Ahlqvist", "given": "Emma", "initials": "E", "orcid": "0000-0002-6513-2384", "researcher": {"href": "https://publications.scilifelab.se/researcher/415b737a7da04f13ab0fd104c375b097.json"}}, {"family": "Smith", "given": "Christopher A", "initials": "CA"}, {"family": "Allen", "given": "Marie", "initials": "M"}, {"family": "Reimann", "given": "Frank", "initials": "F", "orcid": "0000-0001-9399-6377", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d899786a20c44dcbb8aec2e895c6ba9.json"}}, {"family": "Gribble", "given": "Fiona M", "initials": "FM", "orcid": "0000-0002-4232-2898", "researcher": {"href": "https://publications.scilifelab.se/researcher/3381ad13c9464a80bbf910009844722e.json"}}, {"family": "Ohlsson", "given": "Claes", "initials": "C", "orcid": "0000-0002-9633-2805", "researcher": {"href": "https://publications.scilifelab.se/researcher/995dac358caa4a169fc889b7a3eef44a.json"}}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Nilsson", "given": "Peter M", "initials": "PM", "orcid": "0000-0002-5652-8459", "researcher": {"href": "https://publications.scilifelab.se/researcher/f23c2a10ac2a4d73a8f62b94855635f1.json"}}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M", "orcid": "0000-0002-3578-2503", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e54fbe6f0fc4eed93108b382e1b2952.json"}}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "58", "issue": "3", "pages": "540-549", "issn-l": "1061-4036"}, "abstract": "Despite the importance of the gut microbiome to health, the role of human genetic variation in shaping its composition remains poorly understood. Here we report genome-wide association analyses of harmonized metagenomic data from 16,017 adults in four Swedish population-based studies, with replication in 12,652 people from the Norwegian HUNT study. We identified variants in the OR51E1-OR51E2 locus, encoding sensors for microbiome-derived fatty acids, associated with microbial richness. We further identified 15 study-wide significant genetic associations (P < 5.4 \u00d7 10-11) involving eight loci and 14 common bacterial species, of which 11 associations at six loci were replicated. The results confirm previously reported associations at LCT, ABO and FUT2, and provide evidence for new loci MUC12, CORO7-HMOX2, SLC5A11, FOXP1 and FUT3-FUT6, with supporting data from metabolomics and gene expression analyses. Our findings link gut microbial variation genetically to gastrointestinal functions, including enteroendocrine fatty acid sensing, bile composition and mucosal layer composition.", "doi": "10.1038/s41588-026-02512-2", "pmid": "41688638", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12987725"}, {"db": "pii", "key": "10.1038/s41588-026-02512-2"}], "notes": [], "created": "2026-03-19T16:36:11.040Z", "modified": "2026-03-19T16:36:12.549Z"}, {"entity": "publication", "iuid": "fa518182a7dd46c5a42c1e09136ce963", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa518182a7dd46c5a42c1e09136ce963.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa518182a7dd46c5a42c1e09136ce963"}}, "title": "Evolution of hydration in cement blends with incorporation of activated low-kaolinite clays: Insights into the preferred aluminum uptake by C-(A)-S-H", "authors": [{"family": "Hazarika", "given": "Amrita", "initials": "A", "orcid": "0000-0003-3338-4832", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b605437458a49f7a2327da87729c74b.json"}}, {"family": "Huang", "given": "Liming", "initials": "L", "orcid": "0000-0002-0519-6431", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5750b2295e64603817ebdc2b1404ec2.json"}}, {"family": "Figueira", "given": "Joao", "initials": "J", "orcid": "0000-0001-8819-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/140dc66959ac497c9d2ba5190fa32028.json"}}, {"family": "Babaahmadi", "given": "Arezou", "initials": "A", "orcid": "0000-0002-1911-0272", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef14b297bfe04f1c8aa354355982adde.json"}}], "type": "journal-article", "published": "2026-03-00", "journal": {"title": "Cement and Concrete Research", "issn": "0008-8846", "volume": "201", "pages": "108086", "issn-l": null}, "abstract": null, "doi": "10.1016/j.cemconres.2025.108086", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-02-20T12:59:29.995Z", "modified": "2026-02-20T12:59:30.399Z"}, {"entity": "publication", "iuid": "e05c68328fed4b66bdae56b5a53a8183", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e05c68328fed4b66bdae56b5a53a8183.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e05c68328fed4b66bdae56b5a53a8183"}}, "title": "Enrichment of Neural Crest Cells by Antibody Labeling and Flow Cytometry for Single-Cell Transcriptomics in a Lizard.", "authors": [{"family": "Pranter", "given": "Robin", "initials": "R", "orcid": "0000-0003-3615-0281", "researcher": {"href": "https://publications.scilifelab.se/researcher/02c2a85e333a477597ff77429646a0a9.json"}}, {"family": "Patthey", "given": "Cedric", "initials": "C", "orcid": "0000-0002-2627-9578", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b7707e8bd3d4e029fb1e1f43df86ad4.json"}}, {"family": "Feiner", "given": "Nathalie", "initials": "N", "orcid": "0000-0003-4648-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/4dfa523d52b348359775994be5d69640.json"}}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "Evol Dev", "issn": "1525-142X", "volume": "28", "issue": "1", "pages": "e70030", "issn-l": null}, "abstract": "Neural crest cells (NCCs) are a key component of the vertebrate body plan and contribute to a variety of different traits. Recent advances in single-cell transcriptomics (scRNA-seq) have significantly improved our understanding of NCC biology. However, their dynamic migratory behavior and spatiotemporal heterogeneity in the developing embryo pose significant challenges for their identification and isolation. Consequently, most studies of NCCs have been confined to model organisms with established transgenic tools or established methods for in ovo manipulation. To overcome this limitation, we present a novel approach that combines antibody labeling with fluorescence activated cell sorting to enrich for NCCs and we demonstrate the approach in the common wall lizard (Podarcis muralis). Through microscopy, reverse transcription quantitative polymerase chain reaction and single-cell RNA sequencing, we show that the method enriches for NCCs as efficiently as methods relying on transgenic animals. Using this technique, we successfully characterize transcriptional profiles of NCCs in wall lizard embryos. We anticipate that this method can be applied to a wide range of vertebrates that lack transgenic tools, enabling deeper insights into the diverse roles of neural crest cells in development and evolution.", "doi": "10.1111/ede.70030", "pmid": "41709476", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12917300"}], "notes": [], "created": "2026-02-26T15:21:38.415Z", "modified": "2026-03-24T09:08:52.661Z"}, {"entity": "publication", "iuid": "4ae3dd53948e468a890cf7c38b75b085", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ae3dd53948e468a890cf7c38b75b085.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ae3dd53948e468a890cf7c38b75b085"}}, "title": "Discovering and protecting cryptic biodiversity: A case study of a previously undescribed, vulnerable bird species in Japan.", "authors": [{"family": "Saitoh", "given": "Takema", "initials": "T", "orcid": "0000-0003-4982-4724", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ea03b39f2134b55bae9e444bb0e1fe5.json"}}, {"family": "Shipilina", "given": "Daria", "initials": "D", "orcid": "0000-0002-1145-9226", "researcher": {"href": "https://publications.scilifelab.se/researcher/758a7bdbc6654826ab7f06cf3938b5c3.json"}}, {"family": "Xia", "given": "Canwei", "initials": "C", "orcid": "0000-0003-1432-1019", "researcher": {"href": "https://publications.scilifelab.se/researcher/006d6dc9454d4e0db595691b2e0b8cb5.json"}}, {"family": "Zhang", "given": "Lijun", "initials": "L"}, {"family": "Seki", "given": "Shin-Ichi", "initials": "SI", "orcid": "0000-0002-5140-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/c00a2e3811cb4c7c9d591dbf5b6a4aaa.json"}}, {"family": "Olsson", "given": "Urban", "initials": "U"}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P", "orcid": "0000-0001-7182-2763", "researcher": {"href": "https://publications.scilifelab.se/researcher/f426ea7151c546939b707d5ed71e7d04.json"}}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "PNAS Nexus", "issn": "2752-6542", "volume": "5", "issue": "3", "pages": "pgag037", "issn-l": null}, "abstract": "Despite the escalating biodiversity crisis, many species remain unknown to science and may even disappear unnoticed. This is particularly true for many island populations. We illustrate the problem of detecting overlooked species and its consequences by exploring a rare and geographically restricted migratory songbird. We find that this consists of two-hence even rarer-species: the Japanese endemic Ijima's Leaf Warbler Phylloscopus ijimae from the Izu Islands and the Tokara Leaf Warbler from the Tokara Islands. We describe the latter as a new cryptic species, ie one that is morphologically highly similar to, but genetically distinct from, a known species. The genetic divergence is revealed by analyses of nuclear genome-wide and mitochondrial DNA and supported by differences in vocalizations, while the morphological differences are minimal. We evaluate key conservation genomic indicators, showing that both species show low levels of genetic diversity and signs of a decrease of effective population size. Our genome-wide analysis revealed short runs of homozygosity and a low estimated deleterious load, suggesting limited recent inbreeding and possible purging of harmful alleles-indicators of genetic recovery after past demographic fluctuations. Ijima's Leaf Warbler is already classified as Vulnerable as well as a \"Natural Monument\" in Japan, and we propose that the Tokara Leaf Warbler should retain this status, with continued focused monitoring. Our study not only highlights the importance of integrating genomics with taxonomy for uncovering cryptic avian diversity but also provides a critical foundation for future conservation efforts.", "doi": "10.1093/pnasnexus/pgag037", "pmid": "41852645", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12993812"}, {"db": "pii", "key": "pgag037"}], "notes": [], "created": "2026-03-24T08:59:52.573Z", "modified": "2026-03-24T08:59:53.096Z"}, {"entity": "publication", "iuid": "8901ae491c224ece95ecca7bcd0fb242", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8901ae491c224ece95ecca7bcd0fb242.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8901ae491c224ece95ecca7bcd0fb242"}}, "title": "An Equatorial Hemispheric Barrier Shapes the Diversification of Migratory Belenois Butterflies.", "authors": [{"family": "Janiczek", "given": "Anna", "initials": "A", "orcid": "0009-0002-8654-6946", "researcher": {"href": "https://publications.scilifelab.se/researcher/57a0474b15674fb08e3572896dd004ee.json"}}, {"family": "Palah\u00ed", "given": "Aleix", "initials": "A", "orcid": "0000-0002-1373-4949", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee01ff0f2c3746939dbf64a7fca04439.json"}}, {"family": "Dapporto", "given": "Leonardo", "initials": "L", "orcid": "0000-0001-7129-4526", "researcher": {"href": "https://publications.scilifelab.se/researcher/17d272c2c8214d8fb107f095ac656297.json"}}, {"family": "D\u00edaz-Mart\u00ednez", "given": "Gemma", "initials": "G", "orcid": "0009-0003-4084-4734", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbfd1115d0274688a24ca44352e00d6d.json"}}, {"family": "Nazari", "given": "Vazrick", "initials": "V", "orcid": "0000-0001-9064-8959", "researcher": {"href": "https://publications.scilifelab.se/researcher/47148cc85ab042d78cfcaf5b406e3a95.json"}}, {"family": "Garc\u00eda-Berro", "given": "Aurora", "initials": "A", "orcid": "0000-0002-2419-2516", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fdb6dd337074a89bf36e3b06458f042.json"}}, {"family": "Bahleman", "given": "Farid", "initials": "F", "orcid": "0000-0002-5439-0804", "researcher": {"href": "https://publications.scilifelab.se/researcher/f22a3054ef304d08972c52077aeceaa9.json"}}, {"family": "Collins", "given": "Steve C", "initials": "SC"}, {"family": "Akite", "given": "Perpetra", "initials": "P", "orcid": "0000-0002-0302-1822", "researcher": {"href": "https://publications.scilifelab.se/researcher/19097e8ac2ed4f8580906122df0da105.json"}}, {"family": "Braby", "given": "Michael F", "initials": "MF", "orcid": "0000-0002-5438-587X", "researcher": {"href": "https://publications.scilifelab.se/researcher/74c15f10e0aa48488f51ddec5282dfb9.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}, {"family": "Vila", "given": "Roger", "initials": "R", "orcid": "0000-0002-2447-4388", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f9f7ce050d463bb9a67d6970b9428a.json"}}, {"family": "Suchan", "given": "Tomasz", "initials": "T", "orcid": "0000-0002-0811-8754", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b3c7df2089e4060a8ad426a5570654c.json"}}, {"family": "Talavera", "given": "Gerard", "initials": "G", "orcid": "0000-0003-1112-1345", "researcher": {"href": "https://publications.scilifelab.se/researcher/1081486b2353478b8dba3388e819822b.json"}}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "35", "issue": "6", "pages": "e70310", "issn-l": "0962-1083"}, "abstract": "Biogeographic barriers are typically considered prominent geographic features that block or severely restrict dispersal and gene flow. However, mating barriers can also emerge within continuous suitable habitats, driven by ecological or behavioural constraints. Migratory insects show an extraordinary capacity to traverse vast geographic ranges, as well as notable landscape features like mountains, deserts and oceans. Yet, their movements are not unrestricted: they are shaped by seasonal dynamics that dictate the feasibility of migration across these landscapes. Hemisphericity, the existence of inverted seasonal regimes and orientation cues in the two latitudinal hemispheres, has been proposed as a potential abiotic barrier involved in the diversification of migratory insects. Here, we use population genomic data to investigate patterns of diversification in migratory caper butterflies (Belenois spp.) across Africa. We identify a striking phylogeographic break around the equator in Belenois aurota, and emerging population structure between northern and southern African populations in Belenois creona, consistent with migratory divides aligned with hemispheric barriers. These divergences largely predate the Last Glacial Maximum, when major environmental changes such as contractions-expansions of equatorial rainforests and savannahs occurred. This reinforces the hypothesis that long-term abiotic factors, such as hemisphericity, had a role in limiting north-south dispersal. Given the absence of detectable gene flow detected even in sympatric populations of B. aurota in their contact zone in Kenya, Uganda, and Tanzania, we argue that populations from the Northern and Southern Hemispheres represent different species, and reinstate the taxon Belenois syrinx (Wallengren 1860) reinst. stat. for the Southern African lineage. Our findings provide genomic evidence of migratory divides in insects, which surprisingly emerge in the absence of physical barriers in the landscape, highlighting a role of hemisphere-specific adaptations in driving reproductive isolation and diversification in migratory insects.", "doi": "10.1111/mec.70310", "pmid": "41860563", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13004182"}], "notes": [], "created": "2026-03-23T13:39:58.929Z", "modified": "2026-03-23T13:39:59.651Z"}, {"entity": "publication", "iuid": "2c15bfb44c23441faf38bf7406cf4d3b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c15bfb44c23441faf38bf7406cf4d3b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c15bfb44c23441faf38bf7406cf4d3b"}}, "title": "Symbiotic Diversity of Sap-Feeding Auchenorrhyncha (Hemiptera) in the Upland Landscapes of Central Cardamom Mountains, Cambodia.", "authors": [{"family": "Phauk", "given": "Sophany", "initials": "S"}, {"family": "Sin", "given": "Sopha", "initials": "S"}, {"family": "Terenius", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2026-02-28", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "volume": "89", "issue": "1", "issn-l": "0095-3628"}, "abstract": "Auchenorrhyncha (Hemiptera) harbor diverse bacterial symbionts that play critical roles in host nutrition, adaptation and vector competence. However, how symbiotic communities vary across host species and ecological gradients in tropical montane ecosystems remains poorly understood. Here, we characterized the bacterial microbiota of eight auchenorrhynchan species collected from the upland landscapes of the Central Cardamom mountains, Cambodia, using 16S rRNA (V3-V4) amplicon sequencing. In total, 83 individuals representing eight species were analyzed. Across 188 amplicon sequence variants (ASVs), the obligate symbiont Candidatus (Ca.) Karelsulcia muelleri dominated all hosts, although its relative abundance varied substantially. While some species (Anagonalia sp., Changwhania sp. and Mukaria sp.) contained nearly exclusively Karelsulcia, others harbored diverse co-obligate (Ca. Zinderia) and secondary symbionts, including Rickettsia, Wolbachia, Arsenophonus, Spiroplasma, Ca. Symbiodolus, Ca. Lariskella, Pectobacterium and Xylella. Symbiont composition was highly host-specific, with Clovia sp. exhibiting the greatest diversity and Hecalus sp. dominated by Rickettsia. \u03b2-diversity analysis confirmed that host species explained most variation (87%), whereas topographic variables (exposure level and mountain locality) contributed little, although Ca. Symbiodolus in Stirellus sp2. was more frequent at high-exposure sites. Cross-correlation analysis revealed that only a restricted subset of bacterial taxa correlated significantly with plants families, suggesting selective ecological filtering. Notably, Spiroplasma was positively associated with sundew plants (Droseraceae), whereas Pectobacterium showed consistent negative correlations with multiple plant families. Overall, these findings demonstrate that microbiota in Auchenorrhyncha are shaped primarily by host species, with minor influences from environment and plant associations, highlighting the ecological and evolutionary drivers of symbiotic diversity in sap-feeding insects inhabiting tropical mountain landscapes.\n\nThe online version contains supplementary material available at 10.1007/s00248-026-02724-3.", "doi": "10.1007/s00248-026-02724-3", "pmid": "41762238", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12999766"}, {"db": "pii", "key": "10.1007/s00248-026-02724-3"}], "notes": [], "created": "2026-06-01T11:13:46.083Z", "modified": "2026-06-01T11:13:46.087Z"}, {"entity": "publication", "iuid": "0b48959ee84c4ee890a0e427e268d9c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b48959ee84c4ee890a0e427e268d9c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b48959ee84c4ee890a0e427e268d9c6"}}, "title": "Novel activating SNRNP70-ALK fusion in congenital infant-type hemispheric glioma displays clinical response to lorlatinib: a case-report", "authors": [{"family": "Arthur", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0645-6530", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b07104d934d413a9c9546e7e9933051.json"}}, {"family": "Georgantzi", "given": "Kleopatra", "initials": "K"}, {"family": "de St\u00e5hl", "given": "Teresita D\u00edaz", "initials": "TD"}, {"family": "Guan", "given": "Jikui", "initials": "J", "orcid": "0000-0003-1723-0307", "researcher": {"href": "https://publications.scilifelab.se/researcher/a39044157aa7475485fb489a003b63d1.json"}}, {"family": "Oder", "given": "Blaz", "initials": "B", "orcid": "0000-0001-7984-3104", "researcher": {"href": "https://publications.scilifelab.se/researcher/9851f9fc65fc44aea55d0c1567be7887.json"}}, {"family": "Jylh\u00e4", "given": "Cecilia", "initials": "C"}, {"family": "Illies", "given": "Christopher", "initials": "C"}, {"family": "Sandgren", "given": "Johanna", "initials": "J", "orcid": "0000-0001-6776-2649", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d5b6b16fdbe470f83de8748227f8987.json"}}, {"family": "Svoboda", "given": "Jan", "initials": "J"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Sandvik", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-9273-2158", "researcher": {"href": "https://publications.scilifelab.se/researcher/72b8c0bf76054dc8ba15fa80fa78918e.json"}}, {"family": "H\u00e4gerstrand", "given": "Daniel", "initials": "D", "orcid": "0000-0001-7270-0776", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a683cea1874ac290d91c325a648be8.json"}}, {"family": "Hallberg", "given": "Bengt", "initials": "B"}, {"family": "Palmer", "given": "Ruth", "initials": "R", "orcid": "0000-0002-2735-8470", "researcher": {"href": "https://publications.scilifelab.se/researcher/808281ecc2634b66a274895e58a122bd.json"}}, {"family": "Tham", "given": "Emma", "initials": "E", "orcid": "0000-0001-6079-164X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6689dd9aff584082a57398141a538111.json"}}], "type": "journal-article", "published": "2026-02-26", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "10", "issue": "1", "issn-l": null}, "abstract": "We report a child with an antenatally detected brain tumor that progressed over three years' time despite surgery, chemo- and proton therapy. Retrospective whole-genome and transcriptome sequencing with methylation analysis of primary tumor tissue led to the molecular diagnosis infant-type hemispheric glioma, and identified a novel SNRNP70::ALK fusion, providing a therapeutic target for compassionate-use precision treatment with the ALK tyrosine kinase inhibitor lorlatinib. Functional studies confirmed the fusion protein to be expressed and active in the patient's tumor. After two years of therapy, the child has sustained partial tumor regression on MRI and no new neurological symptoms. We conclude that comprehensive multi-omics analyses are required for correct molecular diagnosis in childhood CNS tumors and can radically impact patient outcome by identifying molecular targets for precision treatment.", "doi": "10.1038/s41698-026-01336-x", "pmid": "41748687", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12996540"}, {"db": "pii", "key": "10.1038/s41698-026-01336-x"}], "notes": [], "created": "2026-03-23T15:20:36.846Z", "modified": "2026-03-24T09:13:14.286Z"}, {"entity": "publication", "iuid": "22b56b49adc44dca95b4fd123ed95039", "links": {"self": {"href": "https://publications.scilifelab.se/publication/22b56b49adc44dca95b4fd123ed95039.json"}, "display": {"href": "https://publications.scilifelab.se/publication/22b56b49adc44dca95b4fd123ed95039"}}, "title": "Isotopic insights into long-term socio-economic transformations in prehistoric Kuyavia, Poland", "authors": [{"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141", "orcid": "0000-0003-4676-5802", "researcher": {"href": "https://publications.scilifelab.se/researcher/d372a7903129404c9fb0fdbbee738f74.json"}}, {"family": "Lewis", "given": "Jamie", "initials": "J"}, {"family": "Wiltshire", "given": "Isabel L", "initials": "IL", "orcid": "0009-0002-1681-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a455775963142fcac9dc01182dae358.json"}}, {"family": "Cramp", "given": "Lucy", "initials": "L", "orcid": "0000-0003-2012-2753", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8181ac4ef9148479fd73870aa34aaea.json"}}, {"family": "Giblin", "given": "Julia", "initials": "J"}, {"family": "Krenz-Niedba\u0142a", "given": "Marta", "initials": "M"}, {"family": "\u0141ukasik", "given": "Sylwia", "initials": "S"}, {"family": "Borowska", "given": "Beata", "initials": "B"}, {"family": "Makowiecki", "given": "Daniel", "initials": "D"}, {"family": "Rennwanz", "given": "Joanna", "initials": "J"}, {"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "Goslar", "given": "Tomasz", "initials": "T"}, {"family": "Knowles", "given": "Tim", "initials": "T"}, {"family": "Kristiansen", "given": "Kristian", "initials": "K"}, {"family": "Sj\u00f6gren", "given": "Karl G\u00f6ran", "initials": "KG"}, {"family": "Jakubczak", "given": "Micha\u0142", "initials": "M"}, {"family": "Bednarczyk", "given": "J\u00f3zef", "initials": "J"}, {"family": "B\u0142aszczyk", "given": "Krzysztof", "initials": "K"}, {"family": "Chachlikowski", "given": "Piotr", "initials": "P", "orcid": "0000-0002-2138-2250", "researcher": {"href": "https://publications.scilifelab.se/researcher/264ecd32afc946f4a8140d72152bf275.json"}}, {"family": "Czebreszuk", "given": "Janusz", "initials": "J"}, {"family": "Grossman", "given": "Anna", "initials": "A"}, {"family": "Ignaczak", "given": "Marcin", "initials": "M"}, {"family": "Karczewska-Kaczmarek", "given": "Emilia", "initials": "E"}, {"family": "Ko\u015bko", "given": "Aleksander", "initials": "A"}, {"family": "Makarowicz", "given": "Przemys\u0142aw", "initials": "P"}, {"family": "Nowaczyk", "given": "Szymon", "initials": "S"}, {"family": "Pearson", "given": "Jessica", "initials": "J"}, {"family": "Roma\u0144ska", "given": "Adriana", "initials": "A"}, {"family": "Stanaszek", "given": "\u0141ukasz Maurycy", "initials": "\u0141M"}, {"family": "Szmyt", "given": "Marzena", "initials": "M"}, {"family": "Starzy\u0144ski", "given": "Krzysztof", "initials": "K"}, {"family": "Roffet-Salque", "given": "M\u00e9lanie", "initials": "M"}], "type": "journal-article", "published": "2026-02-25", "journal": {"issn": "2054-5703", "volume": "13", "issue": "2", "title": "R. Soc. open sci.", "issn-l": "2054-5703"}, "abstract": null, "doi": "10.1098/rsos.250968", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-06-01T11:13:54.764Z", "modified": "2026-06-01T11:13:54.946Z"}, {"entity": "publication", "iuid": "6dfc892282ff426f998cbc7c26e3828f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6dfc892282ff426f998cbc7c26e3828f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6dfc892282ff426f998cbc7c26e3828f"}}, "title": "The N-Myc MB0-MBI region interacts specifically and dynamically with the N-lobe of Aurora kinase A.", "authors": [{"family": "Hultman", "given": "Johanna", "initials": "J", "orcid": "0009-0000-8066-228X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd75d9341822427db7b8b8b8510123fd.json"}}, {"family": "Morad", "given": "Vivian", "initials": "V", "orcid": "0000-0001-9665-4532", "researcher": {"href": "https://publications.scilifelab.se/researcher/36505a4d209d4f439785a062205b180c.json"}}, {"family": "Tanner", "given": "Eliane", "initials": "E"}, {"family": "Kenney", "given": "Tristan M G", "initials": "TMG", "orcid": "0000-0001-8242-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/b739b627992645428ea12ed180dab914.json"}}, {"family": "Pietras", "given": "Zuzanna", "initials": "Z", "orcid": "0000-0002-4501-7311", "researcher": {"href": "https://publications.scilifelab.se/researcher/973d7a63037c432db0f7ca9607b8525b.json"}}, {"family": "Khare", "given": "Lalit Pramod", "initials": "LP"}, {"family": "Derbyshire", "given": "Dean", "initials": "D"}, {"family": "Resetca", "given": "Diana", "initials": "D"}, {"family": "Arrowsmith", "given": "Cheryl H", "initials": "CH"}, {"family": "Aili", "given": "Daniel", "initials": "D", "orcid": "0000-0002-7001-9415", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc760610215a4dee9061f28723b97e62.json"}}, {"family": "Ekstr\u00f6m", "given": "Simon", "initials": "S", "orcid": "0000-0002-7694-285X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6416b323664f4126b70067193d7b8347.json"}}, {"family": "Penn", "given": "Linda Z", "initials": "LZ", "orcid": "0000-0001-8133-5459", "researcher": {"href": "https://publications.scilifelab.se/researcher/780529b33355480890244ff1039ea64f.json"}}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-3772-8279", "researcher": {"href": "https://publications.scilifelab.se/researcher/108086b7b06e4247b332ff4a119b97a5.json"}}, {"family": "Ahlner", "given": "Alexandra", "initials": "A", "orcid": "0000-0001-7004-8251", "researcher": {"href": "https://publications.scilifelab.se/researcher/08cd17a1108045b5be32cd492a082453.json"}}, {"family": "Sunnerhagen", "given": "Maria", "initials": "M", "orcid": "0000-0002-0492-5890", "researcher": {"href": "https://publications.scilifelab.se/researcher/3caade7942f84928b12656cb7e5f8493.json"}}], "type": "journal article", "published": "2026-02-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "The intrinsically disordered MYC proteins are master regulators of cellular growth and function, but when deregulated they become cancer drivers. MYC-protein interactions are key to oncogenesis, and while disrupting such interactions would be of significant therapeutic benefit, the intrinsically disordered properties of MYC have dramatically hampered their characterization. Here, we apply an integrated structural biology approach to describe the structure and dynamics of the N-Myc-Aurora A complex, which is critical in neuroendocrine tumor progression. We reveal a functional interaction where multiple binding sites on N-Myc interact with the Aurora A N-lobe. The interaction is governed by aromatic clusters within the conserved MB0 and MBI motifs in N-Myc that interact with Aurora A in a dynamic binding mode that allosterically promotes kinase activation. We show that N-Myc binding to the Aurora A N-lobe can be inhibited by the small-molecule AurkinA, providing opportunity for therapeutical strategies to disrupt this interaction.", "doi": "10.1038/s41467-026-69725-1", "pmid": "41735282", "labels": {"Structural Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12936163"}, {"db": "pii", "key": "10.1038/s41467-026-69725-1"}], "notes": [], "created": "2026-04-07T14:24:57.298Z", "modified": "2026-04-07T14:24:58.191Z"}, {"entity": "publication", "iuid": "e2949002d3f14561814c4d2a6201aa18", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2949002d3f14561814c4d2a6201aa18.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2949002d3f14561814c4d2a6201aa18"}}, "title": "Silicone-Foam Passive Air Samplers for Combined Target and Nontarget Chemical Profiling and Toxicity Assessment of Airborne Exposomes", "authors": [{"family": "Sunyer-Cald\u00fa", "given": "Adri\u00e0", "initials": "A", "orcid": "0000-0001-5134-1196", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3345feac6fd4bf899478cae45137de7.json"}}, {"family": "Xie", "given": "Hongyu", "initials": "H", "orcid": "0000-0002-2422-0492", "researcher": {"href": "https://publications.scilifelab.se/researcher/e038d701867b464f87f94df18e108b42.json"}}, {"family": "Bonnefille", "given": "B\u00e9nilde", "initials": "B", "orcid": "0000-0001-5141-7111", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb5cae7e57b1443a8b296824dc186b04.json"}}, {"family": "Raptopoulou", "given": "Foteini", "initials": "F", "orcid": "0009-0006-2923-2448", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bc964229f224e20893c5b0eac0261d1.json"}}, {"family": "Pesquet", "given": "Edouard", "initials": "E", "orcid": "0000-0002-6959-3284", "researcher": {"href": "https://publications.scilifelab.se/researcher/891cf06dc79d4befadb50970dae19885.json"}}, {"family": "Rian", "given": "May Britt", "initials": "MB", "orcid": "0000-0001-6153-2164", "researcher": {"href": "https://publications.scilifelab.se/researcher/dad5214e19c7402bbbbfe92fda00b82d.json"}}, {"family": "Schlesinger", "given": "Daniel", "initials": "D"}, {"family": "Norman", "given": "Michael", "initials": "M"}, {"family": "Jeon", "given": "Young June", "initials": "YJ", "orcid": "0009-0006-3575-6491", "researcher": {"href": "https://publications.scilifelab.se/researcher/7651a4c25ed44ccaa540b7c1dd3e72ba.json"}}, {"family": "Kim", "given": "Boram", "initials": "B"}, {"family": "Lee", "given": "Seung Bok", "initials": "SB"}, {"family": "Lee", "given": "Ji Eun", "initials": "JE"}, {"family": "Froment", "given": "Jean", "initials": "J", "orcid": "0000-0003-4844-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/6322367545114b6bac92761a16065e1b.json"}}, {"family": "Papazian", "given": "Stefano", "initials": "S", "orcid": "0000-0003-2538-8702", "researcher": {"href": "https://publications.scilifelab.se/researcher/5de990c59ec4460e92c414dbc0ed0b16.json"}}, {"family": "Martin", "given": "Jonathan W", "initials": "JW", "orcid": "0000-0001-6265-4294", "researcher": {"href": "https://publications.scilifelab.se/researcher/f275a68856cb459ebbc933b18c3e315d.json"}}], "type": "journal-article", "published": "2026-02-24", "journal": {"title": "Environ. Sci. Technol.", "issn": "0013-936X", "volume": "60", "issue": "7", "pages": "5628-5644", "issn-l": null}, "abstract": "Polluted air is a major global health risk factor, yet the chemical composition and toxicity of airborne gases and particles remain underexplored due to their complexity and difficulties in sampling. We recently introduced how polydimethylsiloxane (PDMS) foam\u2500or silicone foam\u2500can be synthesized for passive air sampling, enabling simple and cost-effective nontarget chemical profiling of indoor air. Here, we demonstrate expanded applications, indoors and outdoors, with commercial PDMS-foam, including for: (i) wide-scope target analysis of >220 priority substances by quantitative liquid- and gas chromatography-high-resolution mass spectrometry, (ii) microscopic characterization and nontarget profiling of accumulated fine particles, and (iii) effect-guided discovery of harmful substances, combining toxicological data with nontarget analysis in silico. Median method quantification limits were 0.12 ng/mL, 90% of target analytes had absolute recoveries between 70 and 130%, and hazardous substances were discovered, including ethylene glycols, insecticides, and UV filters. Microscopy revealed the accumulation of abundant fine particles, and the automated characterization of the fluorescent fraction revealed that most were <4 \u03bcm. Extracts from outdoor samples reduced human lung cell viability, and multivariate modeling flagged families of potentially toxic substances in a virtual effect-directed analysis. PDMS-foam disks require field calibration to determine their linear sampling rate(s), but current results and applications establish PDMS-foam as a multimodal passive sampler, enabling integrated chemical quantitation, toxicological analysis, and molecular discovery in air.", "doi": "10.1021/acs.est.5c16613", "pmid": "41665526", "labels": {"Exposomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2026-02-11T07:09:54.108Z", "modified": "2026-02-25T13:40:00.058Z"}, {"entity": "publication", "iuid": "815f3d67b39942bda4ef5dce0da35f32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/815f3d67b39942bda4ef5dce0da35f32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/815f3d67b39942bda4ef5dce0da35f32"}}, "title": "Lipid\u2010Facilitated Opening of the ADAM10 Sheddase Revealed by Enhanced Sampling Simulations", "authors": [{"family": "Schahl", "given": "Adrien", "initials": "A", "orcid": "0000-0001-5839-7715", "researcher": {"href": "https://publications.scilifelab.se/researcher/91c1503f32d64435a8df615d167a5c6f.json"}}, {"family": "Haloi", "given": "Nandan", "initials": "N", "orcid": "0000-0003-3542-333X", "researcher": {"href": "https://publications.scilifelab.se/researcher/26d4c3c8db3b441994180b93bc6eda98.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"family": "Zhang", "given": "Shengpan", "initials": "S"}, {"family": "Sattentau", "given": "Quentin James", "initials": "QJ", "orcid": "0000-0001-7170-1937", "researcher": {"href": "https://publications.scilifelab.se/researcher/d78243e447114e179d1aef437cb35717.json"}}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}, {"family": "Delemotte", "given": "Lucie", "initials": "L", "orcid": "0000-0002-0828-3899", "researcher": {"href": "https://publications.scilifelab.se/researcher/2919e3b5cf0f466f980df8fd700bc306.json"}}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ"}], "type": "journal-article", "published": "2026-02-24", "journal": {"title": "Adv Sci (Weinh)", "issn": "2198-3844", "pages": "e15713", "issn-l": null}, "abstract": "ADAM10 is a crucial membrane-bound metalloprotease that regulates cellular physiology by cleaving and releasing membrane-anchored proteins, including adhesion molecules and growth factor precursors, thereby modulating cell signaling, adhesion, and migration. Despite its central role, its activation mechanisms are not fully understood. Here, we model how phosphatidylserine (PS) exposure during apoptosis triggers ADAM10 activation. We confirm that PS externalization is associated with ADAM10-mediated CD43 shedding from the surface of T cells. Intriguingly, ADAM10 activation correlated with loss of ADAM10 monoclonal antibody binding, suggesting a PS-induced conformational change that alters epitope accessibility. To explore this lipid-mediated conformational change of ADAM10, we employed molecular dynamics simulations to map its conformational landscape. Our simulations revealed that in the absence of PS, ADAM10 samples predominantly closed and intermediate states. By contrast, the presence of PS destabilizes the closed conformation, thereby favoring open states. We provide a mechanistic explanation for this PS-induced conformational change, which drives ADAM10 activation and loss of mAb binding through conformational change. These findings offer new insights into the lipid-mediated regulation of ADAM10 and its conformational dynamics.", "doi": "10.1002/advs.202515713", "pmid": "41733033", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [], "notes": [], "created": "2026-02-25T19:59:11.014Z", "modified": "2026-03-24T09:09:06.921Z"}, {"entity": "publication", "iuid": "5d87b6dd1cac4792b7e1a9fb481823fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d87b6dd1cac4792b7e1a9fb481823fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d87b6dd1cac4792b7e1a9fb481823fc"}}, "title": "Antibiotic resistance gradient along a large Scandinavian river influenced by wastewater treatment plants.", "authors": [{"family": "G\u00f3mez-Mart\u00ednez", "given": "Daniela", "initials": "D", "orcid": "0000-0001-8834-8930", "researcher": {"href": "https://publications.scilifelab.se/researcher/3013d785572c4733822446d664e538a0.json"}}, {"family": "Ngou", "given": "Judith Sorel", "initials": "JS"}, {"family": "Ugolini", "given": "Valentina", "initials": "V"}, {"family": "Lai", "given": "Foon Yin", "initials": "FY"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Corcoll", "given": "Nat\u00e0lia", "initials": "N"}], "type": "journal article", "published": "2026-02-19", "journal": {"title": "FEMS Microbiol. Ecol.", "issn": "1574-6941", "volume": "102", "issue": "3", "issn-l": "0168-6496"}, "abstract": "Recent studies have identified the environment as a key reservoir from which antibiotic resistance genes (ARGs) can be acquired and transmitted to pathogens. However, our knowledge about the presence of ARGs in high-flow river sediments is still limited. We analyzed the resistome of sediment bacterial communities along the Swedish river G\u00f6ta \u00c4lv and investigated the potential dissemination of ARGs and antimicrobials from effluents of wastewater treatment plants (WWTPs). While we detected nine different antimicrobials in the effluent water from the WWTPs through HPLC-MS, their presence was not observed in the river surface water. Analysis by qPCR revealed that the genes sul1 and ermB were the most dominant ARGs among sediment, sludge, and effluent samples. Shotgun metagenomics revealed unique differences between the sludge resistomes of the WWTPs. Moreover, our findings show that ARGs increase downstream of the G\u00f6ta \u00c4lv and their diversity differs from that of the upstream sites. Efflux pump resistance-related genes were most abundant in sediment samples, and beta-lactams and tetracyclines were the most common antibiotic classes targeted by ARGs. Our study emphasizes the importance of urban river sediments as a reservoir of ARGs, as tracking ARGs in WWTPs and their receiving environments improves our understanding of their spread and characteristics.", "doi": "10.1093/femsec/fiag007", "pmid": "41632094", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12917318"}, {"db": "pii", "key": "8456379"}], "notes": [], "created": "2026-06-01T08:42:58.103Z", "modified": "2026-06-01T08:42:58.173Z"}, {"entity": "publication", "iuid": "5f52c18408484928a5bdac12a356745d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f52c18408484928a5bdac12a356745d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f52c18408484928a5bdac12a356745d"}}, "title": "Genetic relatedness mattered in the co-burial ritual of Neolithic hunter-gatherers.", "authors": [{"family": "Mattila", "given": "Tiina Maria", "initials": "TM", "orcid": "0000-0002-1298-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dbb4f417ab0440fb02a305aaf81b3d5.json"}}, {"family": "Fraser", "given": "Magdalena", "initials": "M", "orcid": "0000-0003-4714-088X", "researcher": {"href": "https://publications.scilifelab.se/researcher/de8d9acba81e4da4a1efc097e53aa4f3.json"}}, {"family": "Koelman", "given": "Julian", "initials": "J"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Ivarsson-Aalders", "given": "Marieke", "initials": "M", "orcid": "0009-0001-5174-1840", "researcher": {"href": "https://publications.scilifelab.se/researcher/4df153464673466faa2249a0ef253d82.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Wallin", "given": "Paul", "initials": "P", "orcid": "0000-0002-0916-6264", "researcher": {"href": "https://publications.scilifelab.se/researcher/aac2463e759342bdba70ea7e40caebe2.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}], "type": "journal article", "published": "2026-02-18", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "volume": "293", "issue": "2065", "issn-l": "0962-8452"}, "abstract": "Kin relations among past societies can offer valuable information about the social dynamics of the population. Genetic data from prehistoric human remains can reveal genetic relatedness, and when combined with archaeological information, shed light on social factors shaping ancient communities. However, accessing such information on ancient hunter-gatherer societies has been challenging owing to the scarcity of temporally overlapping multi-burial sites. Here, we focused on the Pitted Ware Culture (PWC) cemetery from Ajvide (Gotland, Sweden), one of Stone Age Europe's largest and best-preserved hunter-gatherer burial grounds of the European Stone Age. We generated new genomic data from 10 individuals, primarily from co-burial contexts, and combined these with published genomes from 24 individuals across four PWC sites on Gotland. The genetic analyses revealed dual ancestry of the Gotlandic PWC, showing approximately 80% ancestry associated with earlier Mesolithic hunter-gatherer groups and 20% with farmer groups. We also identified close genetic relatives between the different studied PWC sites on Gotland, indicating mixing of the groups. All individuals buried together were closely related to one another, including first-, second- and third-degree relatives, and showed significantly elevated genetic relatedness. This demonstrates that genetic relatedness played a defining role in the co-burial ritual and extended beyond first-degree relatives.", "doi": "10.1098/rspb.2025.0813", "pmid": "41705298", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "480372"}], "notes": [], "created": "2026-06-01T08:42:52.357Z", "modified": "2026-06-01T08:42:52.890Z"}, {"entity": "publication", "iuid": "b7284178e7704139b443a0f9e1f75614", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7284178e7704139b443a0f9e1f75614.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7284178e7704139b443a0f9e1f75614"}}, "title": "Homologous recombination deficiency in primary ER-positive and HER2-negative breast cancer.", "authors": [{"family": "Davies", "given": "Helen R", "initials": "HR", "orcid": "0000-0001-6381-3664", "researcher": {"href": "https://publications.scilifelab.se/researcher/e02b6738c9e140858456e24cef5d6b42.json"}}, {"family": "Black", "given": "Daniella", "initials": "D"}, {"family": "Kvist", "given": "Anders", "initials": "A", "orcid": "0000-0002-1358-0695", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e6b39bdc00c442f94caed782772a278.json"}}, {"family": "Sigurj\u00f3nsd\u00f3ttir", "given": "Krist\u00edn", "initials": "K"}, {"family": "Bosch", "given": "Ana", "initials": "A"}, {"family": "Bowden", "given": "Ramsay", "initials": "R", "orcid": "0000-0003-1138-4452", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b6effa9663145dabd83b3ced199385c.json"}}, {"family": "Memari", "given": "Yasin", "initials": "Y"}, {"family": "Chen", "given": "Ziqian", "initials": "Z"}, {"family": "Rinaldi", "given": "Giuseppe", "initials": "G", "orcid": "0000-0002-5650-6049", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7f30b3dfa5489ba61afa7840bc34c7.json"}}, {"family": "Rosengren", "given": "Frida", "initials": "F"}, {"family": "Nacer", "given": "Deborah F", "initials": "DF", "orcid": "0000-0002-7117-1371", "researcher": {"href": "https://publications.scilifelab.se/researcher/e484e25cfdf64d27842357355409dbfc.json"}}, {"family": "Veerla", "given": "Srinivas", "initials": "S", "orcid": "0000-0001-7328-6239", "researcher": {"href": "https://publications.scilifelab.se/researcher/c203a0b3112f4f499ccc79db3e47b303.json"}}, {"family": "Hohmann", "given": "Lennart", "initials": "L", "orcid": "0000-0002-0281-7140", "researcher": {"href": "https://publications.scilifelab.se/researcher/b605a3b893a24a238b5bb6eddd27b672.json"}}, {"family": "Nordborg", "given": "Nicklas", "initials": "N"}, {"family": "H\u00e4kkinen", "given": "Jari", "initials": "J", "orcid": "0000-0002-8466-9179", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b8605b9a7c74b20986146f020cf4b8f.json"}}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J", "orcid": "0000-0002-2195-0385", "researcher": {"href": "https://publications.scilifelab.se/researcher/648fa1d04cb640858fe3534d04cd04d1.json"}}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0002-5793-132X", "researcher": {"href": "https://publications.scilifelab.se/researcher/127501d4e0854d14a4120acee9042bb7.json"}}, {"family": "Nik-Zainal", "given": "Serena", "initials": "S", "orcid": "0000-0001-5054-1727", "researcher": {"href": "https://publications.scilifelab.se/researcher/af746cf472144e1699ee12fa08921c1d.json"}}, {"family": "Staaf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5254-5115", "researcher": {"href": "https://publications.scilifelab.se/researcher/07acbd7f211e4809a8195e2ccf5faf57.json"}}], "type": "journal article", "published": "2026-02-16", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "6", "issue": "1", "pages": "118", "issn-l": null}, "abstract": "Homologous recombination deficiency (HRD) originating from inactivation of genes like BRCA1/BRCA2 is a targetable abnormality common in triple-negative breast cancer (TNBC). In estrogen-receptor (ER)-positive HER2-negative (ERpHER2n) breast cancer (BC), HRD prevalence and clinical impact are unclear.\n\nWe analyzed 502 ERpHER2n tumors from patients recruited via the population-representative Swedish SCAN-B study by whole genome sequencing (WGS), defining mutational signatures-based HRD, as well as matched transcriptional, DNA methylation, clinicopathological, adjuvant treatment, and outcome data.\n\nWe show that HRD is much less frequent in ERpHER2n BC (8.4%) compared to TNBC, though induced by similar genetic/epigenetic mechanisms acting on mainly BRCA1/BRCA2/RAD51C/PALB2 together, providing a plausible HR-inactivation mechanism for 71.4% of HRD tumors. Our modelled estimate of HRD in Western European/Nordic BC is ~10-13%. HRD tumors were observed across all PAM50 gene expression subtypes with the exception of Luminal A tumors ( < 1%) and did not exhibit a unique, defining transcriptional or DNA methylation profile. While HRD status was not statistically associated with differences in patient outcome for patients treated with combined chemotherapy and endocrine therapy, a nonsignificant trend of poorer outcome for patients with HRD tumors was observed for patients treated with adjuvant endocrine therapy only.\n\nERpHER2n HRD tumors show features of aggressive disease, but do not display a distinct transcriptional or DNA methylation profile that clearly differentiates them from HR-proficient tumors. Though numbers are limited, we present early evidence that HRD stratification by WGS could impact therapeutic strategies, as HRD BCs trended to poorer outcomes when not treated with chemotherapy.", "doi": "10.1038/s43856-026-01385-0", "pmid": "41699108", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12909304"}, {"db": "pii", "key": "10.1038/s43856-026-01385-0"}], "notes": [], "created": "2026-06-01T11:12:58.568Z", "modified": "2026-06-01T11:12:58.707Z"}, {"entity": "publication", "iuid": "0f47f664e3e4473d9f72b07bc5730cd2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f47f664e3e4473d9f72b07bc5730cd2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f47f664e3e4473d9f72b07bc5730cd2"}}, "title": "Distinct radial glia subtypes regulate midbrain dopaminergic neuron development.", "authors": [{"family": "\u00c1sgr\u00edmsd\u00f3ttir", "given": "Emil\u00eda Sif", "initials": "ES", "orcid": "0000-0003-1509-6853", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8fc060425ec4835b3bbef9ef2eb90a1.json"}}, {"family": "Bassini", "given": "Luca Fusar", "initials": "LF", "orcid": "0009-0005-8256-8074", "researcher": {"href": "https://publications.scilifelab.se/researcher/69009a47fd394ed5ac1372076eb1be28.json"}}, {"family": "Sun", "given": "Ting", "initials": "T", "orcid": "0000-0002-7104-7215", "researcher": {"href": "https://publications.scilifelab.se/researcher/521fca43267242fca06da0f5fc823e6a.json"}}, {"family": "Puigsasllosas Pastor", "given": "Cl\u00e0udia", "initials": "C", "orcid": "0009-0007-6498-5223", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ee97e4af1854228ab68a0bc94619ef3.json"}}, {"family": "di Val Cervo", "given": "Pia Rivetti", "initials": "PR", "orcid": "0000-0001-5999-1230", "researcher": {"href": "https://publications.scilifelab.se/researcher/45578a8b146d4eaf8b7f5e1391e6a5e3.json"}}, {"family": "Gyllborg", "given": "Daniel", "initials": "D"}, {"family": "Lee", "given": "Kawai", "initials": "K"}, {"family": "Grigsby", "given": "Christopher L", "initials": "CL", "orcid": "0000-0002-0105-3847", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4407a0f102b4ee596d7944155d9226e.json"}}, {"family": "Jude", "given": "Baptiste", "initials": "B", "orcid": "0000-0002-5506-2482", "researcher": {"href": "https://publications.scilifelab.se/researcher/60e0f4af135c4eff99a95ff1cac825bb.json"}}, {"family": "Abaurre", "given": "Carmen", "initials": "C", "orcid": "0000-0002-7800-2829", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a55672674314bf593124300d5c2840f.json"}}, {"family": "Islam", "given": "Saiful", "initials": "S"}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Villaescusa", "given": "Carlos", "initials": "C"}, {"family": "Salt\u00f3", "given": "Carmen", "initials": "C"}, {"family": "Barker", "given": "Roger A", "initials": "RA", "orcid": "0000-0001-8843-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/125769a66f77471da6266577717a6395.json"}}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}, {"family": "Castelo-Branco", "given": "Goncalo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}, {"family": "La Manno", "given": "Gioele", "initials": "G", "orcid": "0000-0003-1428-8757", "researcher": {"href": "https://publications.scilifelab.se/researcher/2dab6b6e789a46eba434ceadf38b6601.json"}}, {"family": "Toledo", "given": "Enrique M", "initials": "EM", "orcid": "0000-0002-1460-4708", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa05854e643c499c8efe6781d3457167.json"}}, {"family": "Arenas", "given": "Ernest", "initials": "E", "orcid": "0000-0003-0197-6577", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3bb18ad1c4b4dae99b60ab0ae13e36a.json"}}], "type": "journal article", "published": "2026-02-16", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256"}, "abstract": "Understanding the development of midbrain dopaminergic (mesDA) neurons is essential for advancing cell replacement therapies for Parkinson's disease. In the developing ventral midbrain (VM), radial glia (Rgl) cells are the progenitors of mesDA neurons. However, distinct Rgl subtypes have recently been identified, and their individual roles are unclear. Here we analyze transcriptomic data from mouse and human VM Rgl to define their contributions to mesDA neuron development. We identify Rgl1 as the progenitor of the mesDA lineage, and reveal a Rgl1 transcriptional network coordinated by BMAL1, which we validate as a new regulator of mesDA neurogenesis. Moreover, we uncover Rgl3 as a key signaling subtype and show that factors expressed by Rgl3 promote the survival and yield of human stem cell-derived mesDA neurons. Our findings delineate distinct roles of Rgl subtypes, elucidate lineage relationships in the developing VM and uncover new factors that improve the derivation of clinically relevant human mesDA neurons.", "doi": "10.1038/s41593-026-02200-8", "pmid": "41699318", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-026-02200-8"}], "notes": [], "created": "2026-02-26T13:31:00.279Z", "modified": "2026-02-26T13:31:01.932Z"}, {"entity": "publication", "iuid": "43f86786cbb24b618ae7f2e4aff2b849", "links": {"self": {"href": "https://publications.scilifelab.se/publication/43f86786cbb24b618ae7f2e4aff2b849.json"}, "display": {"href": "https://publications.scilifelab.se/publication/43f86786cbb24b618ae7f2e4aff2b849"}}, "title": "Multiomics assessment of lung adenocarcinoma subtypes defined through tumor purity-adjusted DNA methylation.", "authors": [{"family": "Nacer", "given": "Deborah F", "initials": "DF"}, {"family": "Arbajian", "given": "Elsa", "initials": "E"}, {"family": "Veerla", "given": "Srinivas", "initials": "S"}, {"family": "Aine", "given": "Mattias", "initials": "M"}, {"family": "J\u00f6nsson", "given": "Mats", "initials": "M"}, {"family": "Rosengren", "given": "Frida", "initials": "F"}, {"family": "Karlsson", "given": "Anna", "initials": "A"}, {"family": "Salomonsson", "given": "Annette", "initials": "A"}, {"family": "Isaksson", "given": "Sofi", "initials": "S"}, {"family": "Planck", "given": "Maria", "initials": "M"}, {"family": "Staaf", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2026-02-14", "journal": {"title": "Genome Med", "issn": "1756-994X", "volume": "18", "issue": "1", "issn-l": "1756-994X"}, "abstract": "Molecular subtypes of lung adenocarcinoma (LUAD) with varying prognosis and characteristics have been proposed based on one or two-dimensional studies but are not yet implemented into clinical routine. Epigenetic modifications in cancer cells are independent of sequence variants, directly linked to gene and genome regulation, and thus provide important information to guide subclassification efforts.\n\nWe performed in-depth epigenomic profiling of 95 primary LUAD samples from a Swedish discovery cohort with comprehensive clinicopathological, epigenomic, genomic, transcriptomic, proteomic, and metabolomic data. Additionally, we estimated pure tumor cell methylomes using a computational approach. We subdivided the discovery cohort into four epigenetic subtypes, the epitypes, reflecting distinct tumor cell methylation states. Resulting epitypes were contrasted based on clinicopathological and molecular features, and our main findings were validated in two additional primary tumor cohorts totaling over 700 samples.\n\nOf the four DNA methylation epitypes, M1-M4, M1 and M4 were associated with the previously proposed mRNA subtypes Terminal Respiratory Unit and Proximal Proliferative, respectively. Epitypes M2 and M3 showed similar mRNA/protein subtype composition but differed with respect to e.g., higher expression of the LUAD histology-associated NAPSA/surfactant metabolism expression metagene in M3. Genes included in this metagene showed lower DNA methylation in M3, counter to a global tendency towards promoter hypermethylation in this epitype. To further delineate tumor intrinsic links between the epigenomic and expression phenotypes, 62 LUAD cell lines classified into the four epitypes were investigated and recapitulated several characteristics from the tumor epitypes, such as methylation and expression pattens of NAPSA/surfactant genes, highlighting epigenetic states as likely drivers or maintainers of broad tumor phenotypes and differentiation states.\n\nDissecting LUAD based on combined biological characteristics using multiomics data has deepened our understanding of the heterogeneity in this complex disease and the mechanisms underlying phenotype formation and maintenance. There remains a critical need for large, publicly accessible, well-annotated multiomic LUAD cohorts to support rigorous subtype discovery and validation, particularly those linked to targeted therapy trial outcomes.\n\nThe online version contains supplementary material available at 10.1186/s13073-026-01609-x.", "doi": "10.1186/s13073-026-01609-x", "pmid": "41691315", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12927254"}, {"db": "pii", "key": "10.1186/s13073-026-01609-x"}], "notes": [], "created": "2026-06-01T11:12:56.465Z", "modified": "2026-06-01T11:12:56.469Z"}, {"entity": "publication", "iuid": "f8a7ffd49cad48eb8cb108d82f8b32ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8a7ffd49cad48eb8cb108d82f8b32ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8a7ffd49cad48eb8cb108d82f8b32ab"}}, "title": "Exploring microbial diversity using cell-size fractionated enrichment incubations from subsurface aquifers at \u00c4sp\u00f6, Sweden.", "authors": [{"family": "Westmeijer", "given": "George", "initials": "G", "orcid": "0000-0002-5529-2237", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2146c3e286d4f858efb5787cb3c74a2.json"}}, {"family": "Turner", "given": "Stephanie", "initials": "S", "orcid": "0009-0007-1915-0139", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f779055bf334226a996f214182b41fc.json"}}, {"family": "Hevele", "given": "Patrik", "initials": "P"}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M", "orcid": "0000-0002-1108-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3eca2f7212a4c67bd7b251fa93848e1.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2026-02-14", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642"}, "abstract": "The continental subsurface hosts energy-constrained groundwaters with a high diversity of ecologically elusive microorganisms adapted to the prevailing low-energy conditions. This study explored potential interactions among microbes using anaerobic enrichment incubations with three types of groundwater of contrasting hydrochemistry from the \u00c4sp\u00f6 Hard Rock Laboratory, Sweden. Removing cells larger than 0.45 \u00b5m from the inoculum resulted in incubations enriched in populations characterized by very small genomes, including Patescibacteria, Nanobdellota, and Omnitrophota. These incubations had a higher diversity than non-fractionated incubations. However, cell numbers and community structure of the fractionated incubations did not change over an incubation period up to four months, despite high microbial diversity and experimental amendments with either simple (acetate) or more complex (cell lysate) carbon sources. In addition, network analysis on the groundwaters revealed multiple co-occurrences between populations affiliated with the Patescibacteria and the Desulfobacterota. Overall, these findings support that a considerable part of microbial diversity has a small cell size in these low energy groundwaters and strong co-occurrences among populations as an important survival strategy.", "doi": "10.1038/s42003-026-09706-8", "pmid": "41691100", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-026-09706-8"}], "notes": [], "created": "2026-02-26T13:35:39.634Z", "modified": "2026-02-26T13:35:39.923Z"}, {"entity": "publication", "iuid": "833c3f2b059a4f12856d43fb4a7e02e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/833c3f2b059a4f12856d43fb4a7e02e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/833c3f2b059a4f12856d43fb4a7e02e3"}}, "title": "Rare germline variants contribute to glioma predisposition: Whole-genome analysis of a regional cohort of glioma patients.", "authors": [{"family": "Rosenbaum", "given": "Adam", "initials": "A", "orcid": "0009-0003-4573-5174", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e6fcd448d744a99945a361353add88f.json"}}, {"family": "Wibom", "given": "Carl", "initials": "C"}, {"family": "Hammermeister Suger", "given": "Austin", "initials": "A", "orcid": "0000-0002-6599-2202", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d5c4526d1504762a430373285155fab.json"}}, {"family": "Pensch", "given": "Raphaela", "initials": "R", "orcid": "0000-0002-0313-8369", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bfb52298bf146c9a327c2fbe2e5e7cb.json"}}, {"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Br\u00e4nnstr\u00f6m", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4201-8204", "researcher": {"href": "https://publications.scilifelab.se/researcher/086ede39254945288fb9c708f98eb0cd.json"}}, {"family": "Rentoft", "given": "Matilda", "initials": "M"}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Lindstr\u00f6m", "given": "Sara", "initials": "S"}, {"family": "Dahlin", "given": "Anna Margareta", "initials": "AM"}, {"family": "Melin", "given": "Beatrice", "initials": "B", "orcid": "0000-0002-9982-3757", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ee34db763294de2b7dec15a9ffe8aee.json"}}], "type": "journal article", "published": "2026-02-12", "journal": {"title": "Neurooncol Adv", "issn": "2632-2498", "volume": "8", "issue": "1", "pages": "vdag038", "issn-l": null}, "abstract": "Gliomas are the most common malignant primary tumor of the central nervous system and show a high mortality, particularly at higher grades. Cancer predisposition syndromes and common low-penetrance single nucleotide polymorphisms have been shown to contribute to glioma risk, but the contribution of rare germline variants remains incompletely understood. Here, we investigated rare germline variants in glioma patients.\n\nWe performed whole-genome sequencing on 113 glioma patients from Northern Sweden, analyzing rare germline variants across 651 genes. Variants were compared to population controls (ACpop, gnomAD) and validated in TCGA glioma data, a UK Biobank glioma nested case-control study, and a separate cohort of 105 Swedish glioblastomas.\n\n17.6% of glioma cases carried a Pathogenic or Likely Pathogenic (P/LP) variant within 1 of the 651 genes, and the number of alleles carrying a P/LP was significantly more than in the reference data (P = ). Many of the observed candidate genes also harbored P/LP variants in our Swedish validation cohort. Overall, gene-based comparison of rare coding variants indicated an enrichment in several genes, including 3.2 \u00d7 10 - 3TP53, CREBBP, and DNMT3A.\n\nRare P/LP germline variants were more frequent among glioma patients than in the reference population within our predefined gene set. These results suggest a contribution of rare germline variants to glioma risk, particularly in genes involved in DNA repair. While several genes are indicated as enriched with rare variants, only TP53 validates across all 3 patient sets.", "doi": "10.1093/noajnl/vdag038", "pmid": "41878702", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13007284"}, {"db": "pii", "key": "vdag038"}], "notes": [], "created": "2026-03-26T20:20:23.541Z", "modified": "2026-03-26T20:20:24.274Z"}, {"entity": "publication", "iuid": "d029c59777c84c9bad57d48f2ef1f8a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d029c59777c84c9bad57d48f2ef1f8a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d029c59777c84c9bad57d48f2ef1f8a0"}}, "title": "Efficacy of mebendazole in the spontaneous NZBxNZWF1 animal model of systemic lupus erythematosus.", "authors": [{"family": "Eloranta", "given": "M L", "initials": "ML"}, {"family": "Nygren", "given": "P", "initials": "P"}, {"family": "Larsson", "given": "R", "initials": "R"}, {"family": "Loskog", "given": "A", "initials": "A"}, {"family": "Woodworth", "given": "N", "initials": "N"}, {"family": "Hultqvist", "given": "M", "initials": "M"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Gravenfors", "given": "Ylva", "initials": "Y"}, {"family": "R\u00f6nnblom", "given": "L", "initials": "L"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}], "type": "journal article", "published": "2026-02-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "pages": "6357", "issn-l": "2045-2322"}, "abstract": "Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with a complex etiology involving both innate and adaptive immune dysregulation. Among several perturbed signaling pathways, decreased ERK activity in CD4\u207a T-cells has been linked to DNA hypomethylation and aberrant gene expression in SLE. Mebendazole (MBZ), an anti-helminthic drug with a well-established safety profile, has shown immunomodulatory effects in preclinical studies, including activation of the MEK/ERK pathway and inhibition of MAPK14 (p38), a known driver of inflammation. To evaluate the therapeutic potential of MBZ in SLE, we tested its efficacy in NZBxNZWF1 mice, a spontaneous and well-characterized SLE model. MBZ treatment resulted in reduced proteinuria, lower anti-dsDNA antibody levels, and diminished glomerular IgG deposition, both in preventive and therapeutic settings. Exploratory in vitro data suggest that MBZ may also influence ERK signaling in B cells, while the mechanistic basis of these effects remains to be clarified. Our findings demonstrate robust phenotypic improvements and support further investigation of MBZ as a repositioned candidate for SLE.\n\nThe online version contains supplementary material available at 10.1038/s41598-026-37930-z.", "doi": "10.1038/s41598-026-37930-z", "pmid": "41680254", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12905218"}, {"db": "pii", "key": "10.1038/s41598-026-37930-z"}], "notes": [], "created": "2026-05-14T20:14:52.517Z", "modified": "2026-05-14T20:14:52.521Z"}, {"entity": "publication", "iuid": "a4925370cf2840a29d01394990c7cb68", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a4925370cf2840a29d01394990c7cb68.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a4925370cf2840a29d01394990c7cb68"}}, "title": "Spatial overlap and temporal synchrony between guilds of insect hosts and parasitoids", "authors": [{"family": "van Dijk", "given": "Laura J A", "initials": "LJA", "orcid": "0000-0003-1015-8496", "researcher": {"href": "https://publications.scilifelab.se/researcher/54c9432c19234fd5bc5dfc0a037dae0f.json"}}, {"family": "Goodsell", "given": "Robert M", "initials": "RM", "orcid": "0000-0002-3349-1876", "researcher": {"href": "https://publications.scilifelab.se/researcher/84f42755a394403b95486707bf4a83bd.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Fisher", "given": "Brian L", "initials": "BL", "orcid": "0000-0002-4653-3270", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e4747cc54254e8181f595e6fe21b953.json"}}, {"family": "Iwaszkiewicz\u2010Eggebrecht", "given": "Elzbieta", "initials": "E", "orcid": "0000-0003-1412-1711", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c085bb455d44ceac2f050f5c38f683.json"}}, {"family": "Lukasik", "given": "Piotr", "initials": "P"}, {"family": "Miraldo", "given": "Andreia", "initials": "A", "orcid": "0000-0001-6107-006X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1de25c21dc4c5fb541f4e8766de4b7.json"}}, {"family": "Pe\u00f1a\u2010Aguilera", "given": "Pablo", "initials": "P"}, {"family": "Ronquist", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3929-251X", "researcher": {"href": "https://publications.scilifelab.se/researcher/440662f277ea4756a08a7f5925b3f485.json"}}, {"family": "Roslin", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications.scilifelab.se/researcher/04d92328b67e47ab82257567c07cf12f.json"}}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f9cf8fde705481281edab32bc9156e5.json"}}], "type": "journal-article", "published": "2026-02-10", "journal": {"title": "Journal of Animal Ecology", "issn": "0021-8790", "issn-l": null}, "abstract": "How communities are structured into functional groups and trophic layers is key to understanding ecosystem functioning. Nonetheless, we lack insights about spatiotemporal variation in guild composition of communities and its causes. To investigate spatial and temporal patterns and drivers of variation in insect feeding guilds, we combined data from a nationwide survey of Swedish insects using Malaise traps and DNA metabarcoding with a comprehensive trait database. We assigned species into one of three feeding guilds (phytophages, saprophages, predators) or into one of three associated parasitoid guilds. We then analysed patterns in species richness for each guild. Species richness declined with latitude in all guilds. Beyond this gradient, local variation in species richness matched between hosts and their parasitoids. Yet, hosts and their parasitoids responded differently to habitat. The phenological peak of parasitoid species richness appeared later than the peak of their hosts, but the length of time lags varied among guilds. Spatiotemporal patterns were driven by guild-specific responses to temperature, though much variation remained between seasons and locations even when controlling for temperature. Overall, these patterns suggest that shifts in both climate and land use may alter the synchrony of insect trophic layers, with unknown consequences.", "doi": "10.1111/1365-2656.70228", "pmid": "41665095", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2026-02-27T13:20:10.573Z", "modified": "2026-03-24T09:07:39.535Z"}, {"entity": "publication", "iuid": "d7cadda1f9044aed80babd0395773f5c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7cadda1f9044aed80babd0395773f5c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7cadda1f9044aed80babd0395773f5c"}}, "title": "Genome Sequencing in 19 Families With Bladder Exstrophy and Epispadias Complex Indicates Involvement of the ADGR-Gene Family.", "authors": [{"family": "Nordenskj\u00f6ld", "given": "Agneta", "initials": "A", "orcid": "0000-0001-6638-4631", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ffe8956663241938ad4c01e8f3474ec.json"}}, {"family": "Alm", "given": "Samara", "initials": "S", "orcid": "0000-0002-8339-4783", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d6cb147d9614153ad9b7c64f82d6536.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Cao", "given": "Jia", "initials": "J", "orcid": "0009-0000-4321-8147", "researcher": {"href": "https://publications.scilifelab.se/researcher/f34d15bd603c4a2394cf0ddff9c4af7c.json"}}, {"family": "Anderberg", "given": "Magnus", "initials": "M", "orcid": "0000-0002-4505-338X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7615d8e407d4ce8bc517220db17c2f8.json"}}, {"family": "Barker", "given": "Gillian", "initials": "G"}, {"family": "Matsson", "given": "Hans", "initials": "H"}, {"family": "Holmdahl", "given": "Gundela", "initials": "G"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Lagerstedt-Robinson", "given": "Kristina", "initials": "K", "orcid": "0000-0001-9848-0468", "researcher": {"href": "https://publications.scilifelab.se/researcher/63d275105d9b4253944abaa311c986ee.json"}}], "type": "journal article", "published": "2026-02-10", "journal": {"title": "Am. J. Med. Genet. A", "issn": "1552-4833", "issn-l": "1552-4825"}, "abstract": "Bladder exstrophy and epispadias complex (BEEC) is one of the most severe congenital malformations of the urogenital tract, significantly impacting continence, sexual function, and renal function. To date, the only recurrent genetic aberration identified is the 22q.11.2 microduplication, but several candidate regions and genes including components of the WNT signaling pathway have been proposed. This study aimed to identify additional genes contributing to the pathogenesis of BEEC and to verify previously suggested candidate genes. We performed trio-based whole genome sequencing on 19 individuals with BEEC and their unaffected parents; of those, five carried earlier reported microdeletions. The genome data was also filtered in silico for variants in 204 candidate genes selected from databases, publications, and in-house findings. Variants were prioritized based on allele frequency and predicted functional impact. In 8 of the 19 trios, our findings highlight members of the ADGR-gene family as novel candidate genes for BEEC, alongside other implicated genes such as TRANK1, CSNK1E, IFT122, SDK1, SDK2, and KIF19 and propose two more CNVs as risk factors for BEEC; on chromosome regions 1p36 and 16p11.2. This study identifies novel candidate genes for BEEC within the ADGR gene family. The results also further implicate a complex molecular background of BEEC.", "doi": "10.1002/ajmga.70074", "pmid": "41668247", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2026-02-26T15:18:15.537Z", "modified": "2026-02-26T15:18:16.369Z"}, {"entity": "publication", "iuid": "de111bb9df48495abaad3bd9499c980b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de111bb9df48495abaad3bd9499c980b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de111bb9df48495abaad3bd9499c980b"}}, "title": "MYC modulates TOP2A diffusion to promote substrate detection and activity", "authors": [{"family": "Cameron", "given": "Donald P", "initials": "DP", "orcid": "0000-0002-3175-6965", "researcher": {"href": "https://publications.scilifelab.se/researcher/5048967b73144d169369da2c50f936fd.json"}}, {"family": "Jackson", "given": "Kathryn", "initials": "K"}, {"family": "Loffreda", "given": "Alessia", "initials": "A", "orcid": "0000-0003-4523-5666", "researcher": {"href": "https://publications.scilifelab.se/researcher/9024990fa139415bb8b95415f853857d.json"}}, {"family": "M\u00f6ller", "given": "Carl", "initials": "C", "orcid": "0000-0001-9463-6402", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c1c0ee010cc4b92b80ea7646843efda.json"}}, {"family": "Kuzin", "given": "Vladislav", "initials": "V", "orcid": "0000-0002-7139-1884", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fffd1dd85a049e6bd92b6c68b5f659f.json"}}, {"family": "Mazzocca", "given": "Matteo", "initials": "M", "orcid": "0000-0003-2079-1535", "researcher": {"href": "https://publications.scilifelab.se/researcher/3723fd392c484487a2f3dd6e86e1549e.json"}}, {"family": "Iliopoulou", "given": "Evanthia", "initials": "E"}, {"family": "Kolbeinsdottir", "given": "Hallgerdur", "initials": "H"}, {"family": "Paluda", "given": "Andrej", "initials": "A", "orcid": "0000-0002-0716-0512", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1803d292e10408b9e8ea99349b27e59.json"}}, {"family": "Pavlova", "given": "Evgeniya", "initials": "E"}, {"family": "Jagodic", "given": "Bea", "initials": "B", "orcid": "0009-0005-0997-8130", "researcher": {"href": "https://publications.scilifelab.se/researcher/db2473744b2f45f58531fc7adc0f9bca.json"}}, {"family": "Lopez Duran", "given": "Brian Saidel", "initials": "BS"}, {"family": "Lamour", "given": "Val\u00e9rie", "initials": "V", "orcid": "0000-0001-7793-4029", "researcher": {"href": "https://publications.scilifelab.se/researcher/831fbc98eff844af82760e66cff024ce.json"}}, {"family": "Westerlund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-4767-4868", "researcher": {"href": "https://publications.scilifelab.se/researcher/7afbab9c0cc94ff8bda3b2116039ad8d.json"}}, {"family": "Mazza", "given": "Davide", "initials": "D", "orcid": "0000-0003-2776-4142", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf51d8276b05459ba57162f4da86d020.json"}}, {"family": "Baranello", "given": "Laura", "initials": "L", "orcid": "0000-0001-6039-1849", "researcher": {"href": "https://publications.scilifelab.se/researcher/a33e20ca8e284b5db1cca13e5e6d7940.json"}}], "type": "journal-article", "published": "2026-02-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Topoisomerases alleviate DNA supercoiling by cleaving and resealing DNA strands. Previously, we showed that the oncoprotein MYC recruits and stimulates topoisomerases to remove DNA entanglements generated by oncogenic transcription. Understanding this mechanism may suggest methods to inhibit MYC-driven topoisomerase activation, targeting tumor-specific transcription. Here, we demonstrate that the essential topoisomerase TOP2A in human cells exists in a dynamic equilibrium between sequestration in the nucleolus, substrate searching in transcription hubs, and active engagement on chromatin. This equilibrium is highly responsive to changes in DNA topology, allowing cells to regulate TOP2A levels. Using single molecule tracking, here we show that MYC accelerates TOP2A diffusion in cells. We explain this phenotype by demonstrating that MYC limits TOP2A self-interaction in vitro, while decreasing the size of TOP2A complexes in cells. By increasing TOP2A diffusion, MYC promotes substrate binding and increases TOP2A engagement on chromatin genome-wide, revealing the mechanism underlying MYC stimulation of TOP2A activity.", "doi": "10.1038/s41467-026-69232-3", "pmid": "41663397", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12996632"}, {"db": "pii", "key": "10.1038/s41467-026-69232-3"}], "notes": [], "created": "2026-02-12T07:56:19.235Z", "modified": "2026-03-24T09:07:07.272Z"}, {"entity": "publication", "iuid": "934abbdaa93042c99b863e927fd9b3eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/934abbdaa93042c99b863e927fd9b3eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/934abbdaa93042c99b863e927fd9b3eb"}}, "title": "Targeted CSF metabolomics and conformal prediction improve diagnostic accuracy of normal pressure hydrocephalus.", "authors": [{"family": "Hofling", "given": "Ulrika", "initials": "U"}, {"family": "Jakobsson", "given": "Jenny", "initials": "J"}, {"family": "Erngren", "given": "Ida", "initials": "I"}, {"family": "Ekman", "given": "Oskar", "initials": "O"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Sreenivasan", "given": "Akshai Parakkal", "initials": "AP"}, {"family": "Siljebo", "given": "Jakob", "initials": "J"}, {"family": "Libard", "given": "Sylwia", "initials": "S"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "L\u00f6wenmark", "given": "Malin", "initials": "M"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Kultima", "given": "Kim", "initials": "K"}, {"family": "Virhammar", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2026-02-07", "journal": {"title": "Fluids Barriers CNS", "issn": "2045-8118", "volume": "23", "issue": "1", "issn-l": null}, "abstract": "Idiopathic normal pressure hydrocephalus (iNPH) is a progressive but treatable neurological disorder. Yet, diagnosis is often confounded by overlapping symptoms and biomarker profiles with Alzheimer\u2019s disease (AD), mild cognitive impairment (MCI), and frontotemporal dementia (FTD). We aimed to determine whether cerebrospinal fluid (CSF) metabolomic profiling, combined with uncertainty-aware machine learning using conformal prediction (CP), could improve diagnostic differentiation of iNPH.\n\nCSF samples were collected from 120 patients with iNPH, 44 healthy controls, and 152 individuals with AD, MCI, or FTD. Targeted metabolomics of 59 metabolites was performed using liquid chromatography\u2013high-resolution mass spectrometry. Group differences were assessed using age- and sex-adjusted regression models. Multivariate classification with partial least squares discriminant analysis (PLS-DA) incorporated metabolites, demographics, and conventional biomarkers (amyloid-\u03b242, tau, phosphorylated tau). CP was applied to address individual-level diagnostic uncertainty.\n\nEight metabolites (proline, threonine, histidine, tyrosine, tryptophan, isobutyrylcarnitine, citric acid, and dehydroascorbic acid) were consistently reduced in iNPH (q < 0.05), independent of ventricular volume and cortical tau or amyloid-\u03b2 pathology. An integrated PLS-DA model combining metabolomic, demographic, and AD-biomarker data achieved excellent discrimination (AUC = 0.97). CP provided calibrated case-level confidence, identifying clear-cut and uncertain cases while maintaining high accuracy (94% for iNPH, 97% for not-iNPH).\n\niNPH exhibits a distinct CSF metabolomic signature reflecting altered amino acid metabolism, mitochondrial function, and oxidative stress. Integrating metabolomic data with established biomarkers enhances diagnostic accuracy, while CP adds individualized uncertainty estimates to improve diagnostic confidence and guide treatment decisions.\n\nThe online version contains supplementary material available at 10.1186/s12987-026-00771-z.", "doi": "10.1186/s12987-026-00771-z", "pmid": "41654915", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12930833"}, {"db": "pii", "key": "10.1186/s12987-026-00771-z"}], "notes": [], "created": "2026-04-10T07:10:24.128Z", "modified": "2026-04-10T07:10:24.131Z"}, {"entity": "publication", "iuid": "43121743f286455382be9baac0b2e1c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/43121743f286455382be9baac0b2e1c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/43121743f286455382be9baac0b2e1c9"}}, "title": "Multi-omics data integration from patients with carotid stenosis illuminates key molecular signatures of atherosclerotic instability.", "authors": [{"family": "Das", "given": "Vivek", "initials": "V"}, {"family": "Narayanan", "given": "Sampath", "initials": "S"}, {"family": "Zhang", "given": "Xiang", "initials": "X"}, {"family": "Bergman", "given": "Otto", "initials": "O"}, {"family": "Djordjevic", "given": "Djordje", "initials": "D"}, {"family": "Kronqvist", "given": "Malin", "initials": "M"}, {"family": "Chemaly", "given": "Melody", "initials": "M"}, {"family": "Karadimou", "given": "Glykeria", "initials": "G"}, {"family": "Sundman", "given": "Sofija", "initials": "S"}, {"family": "Prasad", "given": "Inika", "initials": "I"}, {"family": "Buckler", "given": "Andrew J", "initials": "AJ"}, {"family": "Knape", "given": "Karin Conde", "initials": "KC"}, {"family": "Michaelsen", "given": "Natasha Barascuk", "initials": "NB"}, {"family": "Hedin", "given": "Ulf", "initials": "U"}, {"family": "Matic", "given": "Ljubica", "initials": "L"}], "type": "journal article", "published": "2026-02-06", "journal": {"title": "Genome Med", "issn": "1756-994X", "volume": "18", "issue": "1", "issn-l": "1756-994X"}, "abstract": "Understanding the pathophysiology of unstable atherosclerosis is imperative to prevent myocardial infarction and stroke. Here, we used multi-omics integration to identify key molecular targets with diagnostic and therapeutic potential.\n\nBiobank of Karolinska Endarterectomies encompassing patients with symptomatic (S) and asymptomatic (AS) carotid atherosclerosis was the main resource. Plaques, peripheral blood monocytes and plasma sampled locally from around plaque or periphery of n > 700 individuals, were profiled by transcriptomics, proteomics and metabolomics. A supervised machine learning method DIABLO was used for patient data integration. Multi-omics layers were integrated separately across local and peripheral disease sites, and their intersection, with stratification for symptomatology. Identified analytes were investigated using scRNAseq, clinical and outcome data.\n\nIn peripheral circulation, FABP4, IL6, Bilirubin and Sphingomyelin were the most prominent analytes. F11, ANGPTL3, ICOSLG, ITGB1 and Sphingomyelin were enriched in the local disease site, while FABP4, C1R, IL6, Bilirubin and Sphingomyelin appeared at the intersection. Coagulation, necroptosis, inflammation and cholesterol metabolism were confirmed as key pathways determining symptomatology. Clinical analyses showed an impact of lipid-lowering therapy on ICOSLG expression, anti-hypertensives on plasma FABP4 and BLVRB levels, anti-diabetics on plasma Sphingomyelins, while no medications affected ANGPTL3. Association with future adverse events was shown for plasma Bilirubin, Sphingomyelin, ANGPTL3 and ICOSLG plaque levels. Open-source target analyses suggested genetic involvement of F11, C1S, EGFR, IL6, ANGPTL3 in the disease.\n\nUsing an innovative, multi-modal data integration machine learning framework, this study provides confirmatory and novel information on mechanisms behind atherosclerotic instability. The findings raise possibilities for translational prioritizations to aid personalized medicine.\n\nThe online version contains supplementary material available at 10.1186/s13073-026-01601-5.", "doi": "10.1186/s13073-026-01601-5", "pmid": "41652626", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12927228"}, {"db": "pii", "key": "10.1186/s13073-026-01601-5"}], "notes": [], "created": "2026-05-27T11:37:57.073Z", "modified": "2026-05-27T11:37:57.076Z"}, {"entity": "publication", "iuid": "2c3956defcf44e96ad1976508cd8f7ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c3956defcf44e96ad1976508cd8f7ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c3956defcf44e96ad1976508cd8f7ed"}}, "title": "Molecular interactome of HNRNPU reveals regulatory networks in neuronal differentiation and DNA methylation.", "authors": [{"family": "Oksanen", "given": "Marika", "initials": "M", "orcid": "0000-0003-4140-4282", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a8727638dc49fe88b15052d5741fd5.json"}}, {"family": "Mastropasqua", "given": "Francesca", "initials": "F", "orcid": "0000-0003-4237-2446", "researcher": {"href": "https://publications.scilifelab.se/researcher/30aece0009c94ace82728640c71682f7.json"}}, {"family": "Mazan-Mamczarz", "given": "Krystyna", "initials": "K", "orcid": "0009-0005-1545-0500", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c526906891841359c173a86c8ab6414.json"}}, {"family": "Martindale", "given": "Jennifer L", "initials": "JL", "orcid": "0000-0002-3234-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/46adaad64bfc479eb2452956f6a25cc3.json"}}, {"family": "Ye", "given": "Xuan", "initials": "X"}, {"family": "Arora", "given": "Abishek", "initials": "A", "orcid": "0000-0002-6149-4417", "researcher": {"href": "https://publications.scilifelab.se/researcher/384ef4f8d6eb49d6873c87556843a7a2.json"}}, {"family": "Banskota", "given": "Nirad", "initials": "N"}, {"family": "Gorospe", "given": "Myriam", "initials": "M", "orcid": "0000-0001-5439-3434", "researcher": {"href": "https://publications.scilifelab.se/researcher/d946f33774fc424fa0ae365eb8079646.json"}}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba19ec07147743c6942ea10c9a92482a.json"}}], "type": "journal article", "published": "2026-02-05", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "54", "issue": "4", "issn-l": "0305-1048"}, "abstract": "HNRNPU is an RNA-binding protein with diverse roles in transcriptional and post-transcriptional regulation. Pathogenic genetic variants of HNRNPU cause a severe neurodevelopmental disorder (NDD), but the underlying molecular mechanisms are unclear. Here, we comprehensively investigate the HNRNPU molecular interactome by integrating protein-protein interaction (PPI) mapping, RNA target identification, and genome-wide DNA methylation profiling in human neuroepithelial stem cells and differentiating neural cells. We identified extensive HNRNPU-centered networks, including an association with the mammalian SWI/SNF chromatin-remodeling complex, and uncovered a previously unrecognized role in translation. We present evidence that HNRNPU associates with messenger RNAs (mRNAs) encoding proteins important for neuronal development, including several linked to NDDs. Silencing HNRNPU reprogrammed methylation dynamics at regulatory regions, particularly at active and bivalent promoters of neurodevelopmental transcription factors. Integrative analysis across PPI, RNA, and methylome datasets identified 19 converging genes at all three molecular levels, including NDD genes within the SWI/SNF complex, SMARCA4 and SMARCC2, and RNA-processing machinery such as SYNCRIP. Together, these data showcase HNRNPU as a central coordinator of RNA metabolism and epigenetic remodeling during neural differentiation, linking RNA-binding, chromatin organization, and DNA methylation to the pathogenesis of HNRNPU-related NDDs.", "doi": "10.1093/nar/gkag107", "pmid": "41674383", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12895067"}, {"db": "pii", "key": "8474399"}], "notes": [], "created": "2026-02-27T13:05:08.621Z", "modified": "2026-03-24T09:06:45.961Z"}, {"entity": "publication", "iuid": "1f47f9fb4e1e4013a73952ad427c61e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f47f9fb4e1e4013a73952ad427c61e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f47f9fb4e1e4013a73952ad427c61e2"}}, "title": "TGF\u03b2 signaling promotes cell cycle progression and resistance to the CDK4/6 inhibitor palbociclib through SOX4 transcriptional modulation in breast cancer cells.", "authors": [{"family": "Ali", "given": "Mohamad Moustafa", "initials": "MM", "orcid": "0000-0002-4902-0550", "researcher": {"href": "https://publications.scilifelab.se/researcher/780c944670ff4d7489410895569ac257.json"}}, {"family": "Itoh", "given": "Yuka", "initials": "Y"}, {"family": "Badji", "given": "Aisha Mariama Pereira", "initials": "AMP"}, {"family": "Gallant", "given": "Sarah", "initials": "S", "orcid": "0009-0003-9742-4706", "researcher": {"href": "https://publications.scilifelab.se/researcher/666f2f479a3e4421b0aa834d49c0d724.json"}}, {"family": "Tsirigoti", "given": "Chrysoula", "initials": "C", "orcid": "0000-0001-6554-738X", "researcher": {"href": "https://publications.scilifelab.se/researcher/369717d5e92a4045b701964c37fd0aa8.json"}}, {"family": "Bai", "given": "Yu", "initials": "Y", "orcid": "0009-0002-0812-8917", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1f57827cead428f8a7d7e4386eca3a3.json"}}, {"family": "Filipek-G\u00f3rniok", "given": "Beata", "initials": "B"}, {"family": "Miyazawa", "given": "Keiji", "initials": "K", "orcid": "0000-0002-7835-7718", "researcher": {"href": "https://publications.scilifelab.se/researcher/71984836d37c463eaf5ded53bed887dc.json"}}, {"family": "Heldin", "given": "Carl-Henrik", "initials": "CH", "orcid": "0000-0002-9508-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f705f7c509904a1db721ace2267ca48f.json"}}, {"family": "Moustakas", "given": "Aristidis", "initials": "A", "orcid": "0000-0001-9131-3827", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c1626d991f3485e81232db174537e6d.json"}}], "type": "journal article", "published": "2026-02-04", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "volume": "17", "issue": "1", "pages": "209", "issn-l": "2041-4889"}, "abstract": "Cancer signaling encompasses a wide array of entangled molecular cascades that promote oncogenic progression and counteract the effect of tumor suppressors. Transforming growth factor \u03b2 (TGF\u03b2) induces complex and stage-dependent effects throughout tumor progression. During pre-malignant hyperplastic growth, TGF\u03b2 restricts cell proliferation and inflammation, while on the other hand, TGF\u03b2 promotes migration and distal metastasis of cancer cells. To dissect the temporal chromatin-based transcriptional response to TGF\u03b2, we employed 3D culture models of isogenic human breast epithelial cells, exemplified by non-oncogenic MCF-10A (MI) and their HRAS-transformed counterpart (MII). Genome-wide chromatin accessibility profiling revealed an extensive chromatin opening induced by TGF\u03b2 at transcription start sites and enhancer elements in both models, with a marked enrichment of SOX4 binding motifs in oncogenic cells. Transcriptomic analyses unexpectedly revealed the upregulation of DNA replication and DNA damage response pathways, following TGF\u03b2 stimulation of oncogenic MII 3D cultures. Canonical TGF\u03b2-driven programs, including epithelial-mesenchymal transition and metabolic reprogramming, were activated in both models. Notably, single-cell RNA-seq of primary breast tumors confirmed co-expression of SOX4 and cell cycle regulators. Mechanistically, we show that TGF\u03b2 induces the interaction between the MH2 domain of SMAD3 and the intrinsically disordered regions of SOX4, co-activating downstream gene targets. Validating the genome-wide analyses, we found that resistance of breast cancer cells to the CDK4/6 inhibitor palbociclib conferred by TGF\u03b2 stimulation was functionally dependent on SOX4. Collectively, our findings reveal an apparent oncogenic function of TGF\u03b2 in promoting cell cycle progression and drug resistance through SOX4, highlighting the pro-tumorigenic role of TGF\u03b2 signaling in breast cancer progression.", "doi": "10.1038/s41419-026-08435-4", "pmid": "41639049", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12895049"}, {"db": "pii", "key": "10.1038/s41419-026-08435-4"}], "notes": [], "created": "2026-06-01T08:42:55.172Z", "modified": "2026-06-01T08:42:55.598Z"}, {"entity": "publication", "iuid": "d424cf3383cb4f00b90f3c15f327aeae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d424cf3383cb4f00b90f3c15f327aeae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d424cf3383cb4f00b90f3c15f327aeae"}}, "title": "Dual-Color Expansion Microscopy of Membrane Proteins Using Bioorthogonal Labeling", "authors": [{"family": "Edwards", "given": "Steven", "initials": "S", "orcid": "0000-0001-7930-7977", "researcher": {"href": "https://publications.scilifelab.se/researcher/899ddd1ca8b148f696e5d30f30d762b1.json"}}, {"family": "Meineke", "given": "Birthe", "initials": "B", "orcid": "0000-0002-8912-0783", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1cc783424be4fe2b41d82bba5c2a412.json"}}, {"family": "Bauer", "given": "Sebastian", "initials": "S", "orcid": "0009-0009-7265-1527", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46eb06fbcd1476b8d55bd823a46a19c.json"}}, {"family": "Blom", "given": "Hans", "initials": "H", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "Els\u00e4sser", "given": "Simon", "initials": "S", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}], "type": "journal-article", "published": "2026-02-04", "journal": {"title": "Nano Lett.", "issn": "1530-6984", "volume": "26", "issue": "4", "pages": "1321-1326", "issn-l": null}, "abstract": "With recent advances in fluorescence microscopy, resolution is often limited by the size of the label and the resulting linkage error, rather than the microscope itself. Site-specific incorporation of noncanonical amino acids (ncAAs) combined with bioorthogonal click chemistry provides a powerful tool for fluorescent protein labeling, overcoming the spatial uncertainty inherent to antibody-based probes. Here, we present a method to further improve labeling precision by combining ncAA labeling with expansion microscopy (ExM) for dual-color super-resolution imaging. After optimizing labeling procedures and fluorophore selection, we visualize and resolve the nanoscale distribution of Na,K-ATPase \u03b11 and \u03b21 subunits in expanded HEK 293T cells. We validate our approach by super-resolution STED imaging of the ncAA labeled \u03b21 subunit in unexpanded cells. This work presents a strong framework for multiplexed, high-resolution imaging, suggesting that ncAA labeling combined with ExM enables biological imaging at the nanometer scale.", "doi": "10.1021/acs.nanolett.5c05301", "pmid": "41571281", "labels": {"Integrated Microscopy Technologies Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12879918"}], "notes": [], "created": "2026-01-24T20:15:09.343Z", "modified": "2026-02-11T12:54:50.277Z"}, {"entity": "publication", "iuid": "a537001d14d34f14b3048bdf35e0b950", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a537001d14d34f14b3048bdf35e0b950.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a537001d14d34f14b3048bdf35e0b950"}}, "title": "Mechanistic insights into PCBP1-driven unfolding of selected i-motif DNA at G1/S checkpoint.", "authors": [{"family": "Sengupta", "given": "Pallabi", "initials": "P", "orcid": "0000-0002-1413-9412", "researcher": {"href": "https://publications.scilifelab.se/researcher/851c95f648f242e0ba67202279725796.json"}}, {"family": "Gillet", "given": "Natacha", "initials": "N", "orcid": "0000-0002-7657-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce5b43ffd5e44fbe926a3d26064b6760.json"}}, {"family": "Obi", "given": "Ikenna", "initials": "I", "orcid": "0000-0003-0364-8964", "researcher": {"href": "https://publications.scilifelab.se/researcher/e46c65e7b0e540b0a7c225d54c1502d7.json"}}, {"family": "Sabouri", "given": "Nasim", "initials": "N", "orcid": "0000-0002-4541-7702", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bdc688dc85a4932acfdfffad8bfc443.json"}}], "type": "journal article", "published": "2026-02-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "pages": "1149", "issn-l": "2041-1723"}, "abstract": "I-motifs are non-canonical, four-stranded DNA structures in cytosine-rich genomic regions, yet their protein-mediated regulation remains underexplored. Here, we identify PCBP1 (Poly(rC)-binding protein 1) as a selective i-motif-binding protein that unfolds specific i-motifs depending on their protonation and hairpin-forming propensities. Systematic truncation reveals that individual K-homology (KH) domains of PCBP1 cannot selectively bind or unfold i-motifs, but their coordinated actions restore wild-type PCBP1 functions. Using biochemical, biophysical, and molecular dynamics studies, we demonstrate that KH1+2 domains remodel i-motifs, recruiting KH3 to facilitate unfolding and efficient DNA replication. Chromatin and cell-based investigations reveal that PCBP1-knockdown increases i-motif formation at specific genomic loci, coinciding with G1/S arrest and elevated \u03b3H2AX, indicative of genomic instability. During G1/S transition, PCBP1 occupancy peaks at these i-motif loci, ensuring i-motif resolution in early S phase. These findings establish PCBP1 as a critical regulator of i-motif dynamics, directly linking its unfolding activity to G1/S transition and genome stability.", "doi": "10.1038/s41467-026-68822-5", "pmid": "41629296", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-026-68822-5"}, {"db": "pmc", "key": "PMC12865031"}], "notes": [], "created": "2026-02-04T15:32:08.919Z", "modified": "2026-02-04T15:32:09.419Z"}, {"entity": "publication", "iuid": "3857360785ca4b5d9ed1b660982a2c92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3857360785ca4b5d9ed1b660982a2c92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3857360785ca4b5d9ed1b660982a2c92"}}, "title": "Warming Causes a Decline in Baltic Sea Coastal Sediment Microbial Abundance.", "authors": [{"family": "Seidel", "given": "Laura", "initials": "L", "orcid": "0000-0002-2620-914X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0923436cd0a42cea933771b57ae8c94.json"}}, {"family": "Li", "given": "Songjun", "initials": "S", "orcid": "0009-0008-4816-2451", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa0c5a7e34da45c2aca6f8de83af14b5.json"}}, {"family": "Hanna-Elias", "given": "Shahinez", "initials": "S", "orcid": "0009-0007-7894-7287", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a1167e7920f47e188b705992727a776.json"}}, {"family": "Rula", "given": "Iryna", "initials": "I"}, {"family": "Ahlberg", "given": "Louise", "initials": "L", "orcid": "0009-0006-8777-8588", "researcher": {"href": "https://publications.scilifelab.se/researcher/da605765d18c4f5b8bc62bc894b3c3ea.json"}}, {"family": "Forsman", "given": "Anders", "initials": "A", "orcid": "0000-0001-9598-7618", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a605b671cd3414d9c75c2408b74d3de.json"}}, {"family": "Hylander", "given": "Samuel", "initials": "S", "orcid": "0000-0002-3740-5998", "researcher": {"href": "https://publications.scilifelab.se/researcher/47f71565ec50426e9d4893a5335e5fa3.json"}}, {"family": "Ketzer", "given": "Marcelo", "initials": "M", "orcid": "0000-0003-4796-8177", "researcher": {"href": "https://publications.scilifelab.se/researcher/5224e1bded3a4866802b863ed32cb10e.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2026-02-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "28", "issue": "2", "pages": "e70256", "issn-l": "1462-2912"}, "abstract": "Long-term ocean warming impacts the marine environment, and these effects will be exacerbated by future climate change affecting, e.g., biogeochemical processes and microbial communities. However, how the sediment microbial cell abundance and live/dead ratio respond to warming is poorly understood. In this study, sediment core samples were collected from a Baltic Sea bay artificially heated on average 5\u00b0C for > 50 years above a nearby (control) bay unaffected by the heating. Contrary to the expected increased productivity in the heated bay, qPCR-based sediment cell abundances showed decreased cell numbers along the sediment depth gradient in the heated bay compared to the control bay. This could reflect that a portion of the cells' metabolic energy was diverted to a heat related stress response rather than being used for replication. In addition, live/dead cell ratios showed no clear differences in either bay suggesting the majority of the cells were alive. Finally, sediment depth gradient 16S rRNA gene sequencing confirmed previous studies, showing that prolonged warming shallows sediment biogeochemical zones and related microbial communities. In conclusion, future climate change related warming will likely decrease microbial cell abundances that form part of the food web base, potentially impacting the entire ecosystem.", "doi": "10.1111/1462-2920.70256", "pmid": "41712959", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12920023"}], "notes": [], "created": "2026-02-27T07:59:56.449Z", "modified": "2026-02-27T07:59:57.339Z"}, {"entity": "publication", "iuid": "a13b9b2a120741f2af40dbd525b2c748", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a13b9b2a120741f2af40dbd525b2c748.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a13b9b2a120741f2af40dbd525b2c748"}}, "title": "Exploration of immune phenotypes in self-sampling citizens", "authors": [{"family": "Dahl", "given": "Leo", "initials": "L", "orcid": "0000-0003-1492-3052", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4df506f315c4289935b935a503efd56.json"}}, {"family": "Bendes", "given": "Annika", "initials": "A", "orcid": "0000-0001-9329-2353", "researcher": {"href": "https://publications.scilifelab.se/researcher/50dffce4f4444dd8b5ff8f9294146a0b.json"}}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Albrecht", "given": "Vincent", "initials": "V", "orcid": "0009-0003-1985-7733", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d422e623e9e449f98853e6830cdd401.json"}}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "Bj\u00f6rkander", "given": "Sophia", "initials": "S", "orcid": "0000-0002-4600-2883", "researcher": {"href": "https://publications.scilifelab.se/researcher/310af30b841741a790046af03a3cee6d.json"}}, {"family": "Merid", "given": "Simon Kebede", "initials": "SK", "orcid": "0000-0001-5974-7676", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7a04c6538814b089994c7a822ecf07f.json"}}, {"family": "Mezger", "given": "Anja", "initials": "A", "orcid": "0000-0002-7337-9547", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebf61fe41e6f43e4aec2be101de688d4.json"}}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Naluai", "given": "\u00c5sa Torinsson", "initials": "\u00c5T"}, {"family": "Beck", "given": "Olof", "initials": "O"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E", "orcid": "0000-0002-8248-0663", "researcher": {"href": "https://publications.scilifelab.se/researcher/3af5a23ba0a847778eea300f745cb143.json"}}, {"family": "Bauer", "given": "Stefan", "initials": "S"}, {"family": "Gissl\u00e9n", "given": "Magnus", "initials": "M", "orcid": "0000-0002-2357-1020", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b50df8c8ecc45b89574dc76e244b07e.json"}}, {"family": "Roxhed", "given": "Niclas", "initials": "N", "orcid": "0000-0002-7147-6730", "researcher": {"href": "https://publications.scilifelab.se/researcher/3739210caaf14a28898849f20bf6ece5.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal-article", "published": "2026-02-00", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "29", "issue": "2", "pages": "114611", "issn-l": "2589-0042"}, "abstract": "Blood proteins have provided essential insights into how humans responded to the recent pandemic. To expand our understanding beyond patients seeking medical care, we conducted a citizen-centric survey with 2,000 random residents (age: 18-69 years) from Sweden's two largest cities in 2021. With self-sampled dried blood spots (DBS) and health information from 437 (22%) volunteers, we performed multi-analyte COVID-19 serology, measured autoantibodies (AAbs) against 22 interferons, and quantified 502 circulating low-abundant immune-related blood proteins. Antibody assays confirmed self-reported infections (26%) and vaccinations (40%), showed timing-dependent discrepancies in the immune response, and revealed anti-type I interferon AAbs co-occurring frequently alongside natural infections. Proteomics data added plausible mechanistic insights into cell-mediated processes: data-driven analyses revealed 24% of participants presented deviating immune phenotypes linked to infections, immunity, respiratory effects, and age. Multi-molecular DBS analysis of random layperson samples captured the broader spectrum of immune system states, adding relevant insights for clinical and public health investigations.", "doi": "10.1016/j.isci.2025.114611", "pmid": "41630906", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Short read": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12860695"}, {"db": "pii", "key": "S2589-0042(25)02872-X"}], "notes": [], "created": "2026-02-26T13:37:49.302Z", "modified": "2026-03-24T09:13:34.204Z"}, {"entity": "publication", "iuid": "ac574a832b264d6fb5dc1b6f735ae041", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ac574a832b264d6fb5dc1b6f735ae041.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ac574a832b264d6fb5dc1b6f735ae041"}}, "title": "Experimental and machine learning-based exploration of repurposed drugs reveals chemical features underlying phospholipidosis", "authors": [{"family": "Kuzikov", "given": "Maria", "initials": "M", "orcid": "0000-0001-8771-1865", "researcher": {"href": "https://publications.scilifelab.se/researcher/34561b5334f2470396e7ad2a08d8dd72.json"}}, {"family": "Kalman", "given": "Adelinn", "initials": "A"}, {"family": "Karki", "given": "Reagon", "initials": "R"}, {"family": "Reinshagen", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-8080-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/8414f1d0ee0144c88a72beb83f38e21c.json"}}, {"family": "Huchting", "given": "Johanna", "initials": "J"}, {"family": "Qian", "given": "Kun", "initials": "K"}, {"family": "Axelsson", "given": "Hanna", "initials": "H", "orcid": "0000-0003-2365-1749", "researcher": {"href": "https://publications.scilifelab.se/researcher/63b88c4d11c443f39121c6d93fcff1f0.json"}}, {"family": "Tampere", "given": "Marianna", "initials": "M", "orcid": "0000-0001-5744-3206", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c6c86cb20394d17abebb40db23407c8.json"}}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P", "orcid": "0000-0001-5501-466X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0461a910ec4b4faa8668bb4044e76f61.json"}}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B", "orcid": "0000-0001-8658-5967", "researcher": {"href": "https://publications.scilifelab.se/researcher/4645bc97a8024c548111802101b83571.json"}}, {"family": "Gadiya", "given": "Yojana", "initials": "Y", "orcid": "0000-0002-7683-0452", "researcher": {"href": "https://publications.scilifelab.se/researcher/dda537ad863640fbbe1b3e85e05092bb.json"}}, {"family": "Gribbon", "given": "Philip", "initials": "P"}, {"family": "Zaliani", "given": "Andrea", "initials": "A"}], "type": "journal-article", "published": "2026-02-00", "journal": {"title": "Patterns", "issn": "2666-3899", "pages": "101453", "issn-l": null}, "abstract": null, "doi": "10.1016/j.patter.2025.101453", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-02-12T16:13:19.055Z", "modified": "2026-03-24T09:10:21.785Z"}, {"entity": "publication", "iuid": "dfd322f75400494482ef1a0ccf538954", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfd322f75400494482ef1a0ccf538954.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfd322f75400494482ef1a0ccf538954"}}, "title": "SOX21 suppresses glioblastoma growth by repressing AP-1 activity", "authors": [{"family": "Rrapaj", "given": "Eltjona", "initials": "E", "orcid": "0000-0003-3601-4888", "researcher": {"href": "https://publications.scilifelab.se/researcher/40451faaeadb4c29bf77bb83ba383d52.json"}}, {"family": "Yuan", "given": "Juan", "initials": "J"}, {"family": "Kurtsdotter", "given": "Idha", "initials": "I"}, {"family": "Misyurin", "given": "Vsevolod", "initials": "V"}, {"family": "Baselli", "given": "Guido Alessandro", "initials": "GA"}, {"family": "Holmberg", "given": "Johan", "initials": "J", "orcid": "0000-0002-3018-001X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f84bece88a264d228d3770ca634b4a19.json"}}, {"family": "Persson", "given": "Oscar", "initials": "O"}, {"family": "Bergsland", "given": "Maria", "initials": "M"}, {"family": "Muhr", "given": "Jonas", "initials": "J", "orcid": "0000-0003-0704-0788", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a665f02acc432e9d80feb5c61f4572.json"}}], "type": "journal-article", "published": "2026-01-31", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "volume": "17", "issue": "1", "pages": "191", "issn-l": "2041-4889"}, "abstract": "Treatment-resistant glioblastoma stem and precursor cells (GPCs) drive glioblastoma (GBM) growth and recurrence. Thus, targeting the molecular machinery that sustains GPCs in an undifferentiated and self-renewing state is a promising therapeutic strategy. The transcription factor SOX21 effectively suppresses the tumorigenic capacity of GPCs, but the mechanism by which SOX21 impedes GPC features is unknown. By engineering patient-derived GPCs with a transgenic TetOn system we show that SOX21 expression induces an anti-tumorigenic transcriptional program, aligning with clinical data demonstrating a positive correlation between SOX21 levels and improved GBM patient survival. Induced SOX21 expression in GPCs within pre-established GBM reduces their capacity to sustain tumor growth and significantly extends the survival of the orthotopically transplanted mice. Mechanistically, SOX21 functions as a tumor suppressor by binding a large set of AP-1-targeted chromatin regions, leading to epigenetic repression of AP-1-activated genes. Consistently, the anti-tumorigenic activities of SOX21 are largely replicated by AP-1 inhibitors, which decrease GPC proliferation and survival, while overexpression of the AP-1 family member, c-JUN, counteracts these effects. Our findings identify SOX21 as a key regulator that prevents GPC malignancy by targeting and repressing an AP-1-driven, tumor-promoting gene expression program. These results highlight SOX21-regulated pathways as promising therapeutic targets for GBM.", "doi": "10.1038/s41419-026-08442-5", "pmid": "41620461", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12876893"}, {"db": "pii", "key": "10.1038/s41419-026-08442-5"}], "notes": [], "created": "2026-02-06T08:02:53.704Z", "modified": "2026-03-24T09:13:46.564Z"}, {"entity": "publication", "iuid": "2eb354120b4e4f18a6b6912af75d7656", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2eb354120b4e4f18a6b6912af75d7656.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2eb354120b4e4f18a6b6912af75d7656"}}, "title": "Comprehensive profiling of CRISPR/dCas9 epigenome editors indicates a complex link between on and off target effects", "authors": [{"family": "Pahlevan Kakhki", "given": "Majid", "initials": "M", "orcid": "0000-0002-5407-3147", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f376c85cfbe4711ae41d9ee5ade8f09.json"}}, {"family": "Rangani", "given": "Fatemeh", "initials": "F"}, {"family": "Ewing", "given": "Ewoud", "initials": "E", "orcid": "0000-0001-8644-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/aea9350a4f864d8e8781ab111b4f9273.json"}}, {"family": "Starvaggi Cucuzza", "given": "Chiara", "initials": "C", "orcid": "0000-0002-9088-7658", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ead2e8f98754d1586891eda5adb9e1a.json"}}, {"family": "Zheleznyakova", "given": "Galina", "initials": "G"}, {"family": "Kalomoiri", "given": "Maria", "initials": "M"}, {"family": "Kenny", "given": "Lea", "initials": "L"}, {"family": "Raghavan", "given": "Anika", "initials": "A"}, {"family": "Rao Prakash", "given": "Chandana", "initials": "C"}, {"family": "van den Hoeven", "given": "Gabe", "initials": "G"}, {"family": "Venkata S. Badam", "given": "Tejaswi", "initials": "T"}, {"family": "Covacu", "given": "Ruxandra", "initials": "R"}, {"family": "Andreou", "given": "Ioanna", "initials": "I"}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Kular", "given": "Lara", "initials": "L", "orcid": "0000-0002-2907-6071", "researcher": {"href": "https://publications.scilifelab.se/researcher/09563004a20543dc934dd4d3b1ceebd7.json"}}, {"family": "Jagodic", "given": "Maja", "initials": "M", "orcid": "0000-0003-0756-889X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b651ef39c6b0436992e2305f425eba72.json"}}], "type": "journal-article", "published": "2026-01-31", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "issn-l": "1474-7596", "volume": "27", "issue": "1", "pages": null}, "abstract": "CRISPR/dCas9-based epigenome editing systems, including DNA methylation epimodifiers, have greatly advanced molecular functional studies, revolutionizing their precision and applicability. Despite their promise, challenges such as the magnitude and stability of the on-target editing and unwanted off-target effects underscore the need for improved tool characterization and design.\n\nWe systematically compare specific targeting and genome-wide off-target effects of available and novel dCas9-based DNA methylation editing tools over time. We demonstrate that multimerization of the catalytic domain of DNA methyltransferase 3A enhances editing potency but also induces widespread, early methylation deposition at low-to-medium methylated promoter-related regions with specific gRNAs and also with non-targeting gRNAs. A small fraction of the methylation changes associated with transcriptional dysregulation and mapped predominantly to bivalent chromatin associating both with transcriptional repression and activation. Additionally, specific non-targeting control gRNAs cause pervasive and long-lasting methylation-independent transcriptional alterations particularly in genes linked to RNA and energy metabolism. CRISPRoff emerges as the most efficient tool for stable promoter targeting, with fewer and less stable off-target effects compared to other epimodifiers but with persistent transcriptome alterations.\n\nOur findings highlight the delicate balance between potency and specificity of epigenome editing and provide critical insights into the design and application of future tools to improve their precision and minimize unintended consequences.", "doi": "10.1186/s13059-026-03967-6", "pmid": "41620608", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12924462"}, {"db": "pii", "key": "10.1186/s13059-026-03967-6"}], "notes": [], "created": "2026-02-06T08:02:40.826Z", "modified": "2026-03-24T09:10:47.840Z"}, {"entity": "publication", "iuid": "0a1bc06aed8944028dbc6a1adb526828", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a1bc06aed8944028dbc6a1adb526828.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a1bc06aed8944028dbc6a1adb526828"}}, "title": "Skeletal Muscle Microbiopsies in Children and Adults-Tolerability, Sample Yield, and Analyzability.", "authors": [{"family": "H\u00f6gelin", "given": "Emil Rydell", "initials": "ER", "orcid": "0000-0002-0155-6655", "researcher": {"href": "https://publications.scilifelab.se/researcher/a797176a0ef44f38b35727870aa42099.json"}}, {"family": "Edman", "given": "Sebastian", "initials": "S"}, {"family": "Jannig", "given": "Paulo R", "initials": "PR"}, {"family": "L\u00f6fgren", "given": "Axel", "initials": "A"}, {"family": "Thulin", "given": "Kajsa", "initials": "K"}, {"family": "Michno", "given": "Piotr", "initials": "P"}, {"family": "Norrbom", "given": "Jessica", "initials": "J"}, {"family": "Alkner", "given": "Bj\u00f6rn A", "initials": "BA"}, {"family": "von Walden", "given": "Ferdinand", "initials": "F", "orcid": "0000-0003-1134-2252", "researcher": {"href": "https://publications.scilifelab.se/researcher/903e0b7523da4a49960e677009942f67.json"}}, {"family": "Fornander", "given": "Lotta", "initials": "L", "orcid": "0000-0003-2077-8445", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bceecb024cd4adeb8032e41449c7a36.json"}}], "type": "journal article", "published": "2026-01-30", "journal": {"title": "Muscle Nerve", "issn": "1097-4598", "issn-l": null}, "abstract": "Traditional methods of sampling skeletal muscle tissue are invasive. This study aimed to evaluate a sub-millimeter core-biopsy (microbiopsy) as a potentially more tolerable method, with further regard to tissue yield and analyzability of RNA expression.\n\nChildren (9-13 years, n = 11) and adults (18-50 years, n = 16) were recruited. Microbiopsy and venipuncture were performed, with prior application of local anesthesia cream. Additionally, adults underwent a Bergstr\u00f6m muscle biopsy, with infiltrative local anesthesia. Pain was rated using the visual analog scale (VAS), reported as medians (95% CI). Microbiopsy samples were freeze-dried and weighed. To evaluate RNA sequencing performance at low tissue sample weights, a six-step incremental tissue ladder (10-500 \u03bcg) was analyzed.\n\nChildren rated venipunctures and microbiopsies low, at VAS = 0.1 (0.0-0.6) and 1.6 (0.9-3.9), respectively. Microbiopsy pain ratings were slightly higher than venipuncture, p < 0.001. Pain ratings in adults were 0.0 (0.0-0.5), 1.8 (1.3-2.4), 2.9 (2.4-3.8), and 2.7 (2.2-3.8) for venipuncture, microbiopsy, Bergstr\u00f6m biopsy, and infiltrative local anesthesia, respectively. Microbiopsy was rated less painful than Bergstr\u00f6m biopsy and local anesthesia (p < 0.05). Children did not rate microbiopsy more painful than adults (p = 0.82). Microbiopsies yielded on average 303 (SD 121.8) \u03bcg. RNA sequencing detected similar transcriptomic signatures across the tissue ladder.\n\nThe generally low pain ratings for the microbiopsy procedure support its use as a tolerable method of acquiring skeletal muscle samples in both children and adults. It represents a less painful alternative to Bergstr\u00f6m biopsies while still rendering adequate material for RNA sequencing.", "doi": "10.1002/mus.70161", "pmid": "41618578", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2026-02-09T12:51:02.135Z", "modified": "2026-02-09T12:51:03.068Z"}, {"entity": "publication", "iuid": "57ccb7a2e57747c5885ff80d4f036529", "links": {"self": {"href": "https://publications.scilifelab.se/publication/57ccb7a2e57747c5885ff80d4f036529.json"}, "display": {"href": "https://publications.scilifelab.se/publication/57ccb7a2e57747c5885ff80d4f036529"}}, "title": "Single-Cell Comparison of Small Intestinal Neuroendocrine Tumors and Enterochromaffin Cells from Two Patients.", "authors": [{"family": "Axling", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3748-3176", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d84ca11d6f2449583a0fa81eaf1e64c.json"}}, {"family": "Barazeghi", "given": "Elham", "initials": "E"}, {"family": "Hellman", "given": "Per", "initials": "P", "orcid": "0000-0002-5322-5073", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c7a23c0741d444b82657b10fc7a4916.json"}}, {"family": "Norl\u00e9n", "given": "Olov", "initials": "O"}, {"family": "Backman", "given": "Samuel", "initials": "S"}, {"family": "St\u00e5lberg", "given": "Peter", "initials": "P", "orcid": "0000-0002-9625-1394", "researcher": {"href": "https://publications.scilifelab.se/researcher/6698ec6bc9a44d9d84edd62232083ec1.json"}}], "type": "journal article", "published": "2026-01-29", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "18", "issue": "3", "issn-l": "2072-6694"}, "abstract": "Several studies have attempted to identify the initiating drivers of small intestinal neuroendocrine tumor (SI-NET) development and the molecular mechanisms underlying their progression and metastatic spread. Previous gene expression studies have used bulk microarrays or RNA sequencing to compare tumor tissue with normal intestinal mucosa. However, the intestine comprises multiple distinct cell types, and bulk analyses are limited by this cellular heterogeneity, which can confound tumor-specific signals.\n\nWe performed single-cell RNA sequencing on primary SI-NETs and paired normal mucosa from two patients to directly compare tumor cells with their cells of origin, the enterochromaffin (EC) cells. To minimize type I errors, we applied a two-step validation strategy by overlapping differentially expressed genes with an external single-cell dataset and cross-referencing candidate genes for enteroendocrine expression in the Human Protein Atlas.\n\nFor further distinction and characterization, ECs were subdivided into serotonergic and non-serotonergic clusters. This analysis revealed that the SI-NET cells are transcriptionally more similar to serotonergic ECs, consistent with serum metabolite profiles derived from clinical parameters. Our analyses uncovered a loss-of-expression program characterized by regulators of epithelial differentiation and in parallel, a gain-of-expression program displayed neuronal signaling gene induction, implicating functional reprogramming toward neuronal-like properties. Together, these specific losses and gains suggest that our patient-derived SI-NETs undergo adaptation through both loss of enteroendocrine functions and acquisition of neurobiological-promoting signaling pathways.\n\nThese findings nominate candidate drivers for further functional validation and highlight potential therapeutic strategies in our patient cohort, including restoring suppressed Notch signaling and targeting aberrant neuronal signaling networks. However, even with a two-step validation procedure, the modest cohort size limits statistical power and generalizability, particularly for the proposed association to a serotonergic phenotype. Larger, multi-patient single-cell studies are required to confirm these mechanisms and establish their clinical relevance.", "doi": "10.3390/cancers18030435", "pmid": "41681906", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12897003"}, {"db": "pii", "key": "cancers18030435"}], "notes": [], "created": "2026-06-01T08:42:46.361Z", "modified": "2026-06-01T08:42:47.207Z"}, {"entity": "publication", "iuid": "b4356e6f236f4a27b987ac01aea346a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4356e6f236f4a27b987ac01aea346a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4356e6f236f4a27b987ac01aea346a2"}}, "title": "Allergen-specific human IgE isolated through an allergen-agnostic pipeline\u2014understanding immune response and allergen recognition", "authors": [{"family": "Th\u00f6rnqvist", "given": "Linnea", "initials": "L"}, {"family": "Franciskovic", "given": "Eric", "initials": "E"}, {"family": "Godzwon", "given": "Magdalena", "initials": "M", "orcid": "0000-0002-9745-1160", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fa85685e9e149d8a341effcb1b924d0.json"}}, {"family": "Kristensen", "given": "Bjarne", "initials": "B"}, {"family": "Sultan", "given": "Kristin", "initials": "K", "orcid": "0009-0002-5619-517X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7288f4347b8440479e0f908b705f9df5.json"}}, {"family": "Nordstr\u00f6m", "given": "Franziska", "initials": "F", "orcid": "0000-0003-3730-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa587c1b382f4cd1b9486ba50eb8bb0e.json"}}, {"family": "Palmason", "given": "Robert", "initials": "R"}, {"family": "Todorovic", "given": "Nikolina", "initials": "N"}, {"family": "Keller", "given": "Walter", "initials": "W", "orcid": "0000-0002-2261-958X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dfdfb31e5a24ceb93609f4166c06f5c.json"}}, {"family": "Lindstedt", "given": "Malin", "initials": "M", "orcid": "0000-0001-9136-1087", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc58fdfd7f0a40e2bf2fa21c2d2bea36.json"}}, {"family": "Greiff", "given": "Lennart", "initials": "L", "orcid": "0000-0002-7004-1989", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a6c63fee50b446da172ddbb30f69fb2.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}, {"family": "Ohlin", "given": "Mats", "initials": "M", "orcid": "0000-0002-5105-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda1d1ed0b074a04a69b0c8b036dd001.json"}}], "type": "journal-article", "published": "2026-01-28", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "9", "issue": "1", "issn-l": "2399-3642"}, "abstract": "Allergy, characterised by antibody responses of the IgE isotype, is a major health concern. The set of monoclonal human IgE used for studying the molecular mechanisms of allergies is limited. Single-cell sequencing offers opportunities to establish novel antibodies for researching, diagnosis, and treatment of allergies. We describe and exploit a pipeline for generating recombinant IgE directly from the immune repertoires of allergic subjects. It uses single-cell sequencing of IgM- B cells of bone marrow and peripheral blood in an allergen-agnostic manner, combined with high-throughput transcriptome sequencing to identify clonotypes populating the IgE repertoire. Immunochemical and immunoprecipitation analyses are used to deconvolute the specificity of identified antibodies. High-affinity antibodies were raised against four grass pollen allergens, antibodies that illustrated aspects of the development of allergen-specific humoral immunity. The pipeline provides a streamlined approach for the development and characterisation of native allergen-specific antibodies as they occur in allergy and during allergy desensitisation.", "doi": "10.1038/s42003-026-09600-3", "pmid": "41606257", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12953631"}, {"db": "pii", "key": "10.1038/s42003-026-09600-3"}], "notes": [], "created": "2026-02-09T12:51:20.129Z", "modified": "2026-03-24T09:14:00.807Z"}, {"entity": "publication", "iuid": "fe9262efce374c289b2e02bbf47d7a91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe9262efce374c289b2e02bbf47d7a91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe9262efce374c289b2e02bbf47d7a91"}}, "title": "A study of k-mer patterns within DNA molecules sequenced from a chondrite", "authors": [{"family": "Farage", "given": "Carmel", "initials": "C"}, {"family": "Bachelet", "given": "Ido", "initials": "I", "orcid": "0000-0002-1089-1172", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bbc61662c3d4a618655b118166a6005.json"}}], "type": "posted-content", "published": "2026-01-27", "journal": {"issn-l": null}, "abstract": null, "doi": "10.64898/2026.01.26.701670", "pmid": null, "labels": {"Ancient DNA": "Service"}, "xrefs": [], "notes": [], "created": "2026-01-29T12:48:33.188Z", "modified": "2026-01-29T12:48:33.224Z"}, {"entity": "publication", "iuid": "dceda66778b243d48c35e4f210a2f93b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dceda66778b243d48c35e4f210a2f93b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dceda66778b243d48c35e4f210a2f93b"}}, "title": "Effects of incrementally increased plant-based protein intake on gut microbiota and inflammatory-metabolic biomarkers in healthy adults.", "authors": [{"family": "Prado", "given": "Samira", "initials": "S", "orcid": "0000-0003-4627-6291", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9912c2cd66d49a8a067770ef482c755.json"}}, {"family": "Kamm", "given": "Annalena", "initials": "A", "orcid": "0009-0002-9389-4172", "researcher": {"href": "https://publications.scilifelab.se/researcher/478d57e6063e4db89e513430f840207b.json"}}, {"family": "Dannenberg", "given": "Katharina", "initials": "K", "orcid": "0009-0008-1571-0044", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9525504fa7c427b8b19d361d38167c1.json"}}, {"family": "Keidel", "given": "Isabel", "initials": "I", "orcid": "0009-0000-9806-1087", "researcher": {"href": "https://publications.scilifelab.se/researcher/7276d82607474a99905643ac60082036.json"}}, {"family": "Castro-Alves", "given": "Victor", "initials": "V", "orcid": "0000-0002-9535-6821", "researcher": {"href": "https://publications.scilifelab.se/researcher/639528af2bd7482eaca6c998f2df3a94.json"}}, {"family": "Hy\u00f6tyl\u00e4inen", "given": "Tuulia", "initials": "T"}, {"family": "Lentjes", "given": "Marleen", "initials": "M", "orcid": "0000-0003-4713-907X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3579ded172f040698818c7f41ed60525.json"}}, {"family": "Repsilber", "given": "Dirk", "initials": "D"}, {"family": "Marques", "given": "Tatiana M", "initials": "TM"}, {"family": "Brummer", "given": "Robert J", "initials": "RJ"}], "type": "journal article", "published": "2026-01-26", "journal": {"title": "Food Funct", "issn": "2042-650X", "volume": "17", "issue": "2", "pages": "942-956", "issn-l": null}, "abstract": "Shifting to a plant-based diet naturally alters protein source choices. In many countries, protein from yellow pea is widely used as a main ingredient in meat alternatives. Still, its biological effects, especially regarding gastrointestinal health, remain incompletely understood. The aim of our study was to investigate how a weekly increase in the intake of a well-characterized pea protein isolate affects surrogate markers of health, fecal short-chain fatty acids and gut microbiota composition in healthy individuals. Male and female adults (N = 29) participated in this exploratory intervention study. A 4-week pre-intervention period for questionnaires and fecal samples collection was followed by a 4-week supplementation. Participants consumed isolated pea protein in weekly increasing amounts, starting from 0.25 g per kg body mass per day in week 5 to 1.00 g per kg body mass per day in week 8. Questionnaire data, fecal samples as well as fasting blood and 24 h urine samples were collected weekly. Data from biological samples and questionnaires confirmed a healthy study population and compliance. Fecal calprotectin levels significantly increased only in a subset of participants, which was accompanied by higher fecal water cytotoxicity in vitro. Short-chain fatty acids mainly rose in those subjects with stable calprotectin levels. Relative abundances of Limosilactobacillus frumenti, Odoribacter splanchnicus and Lactobacillus crispatus increased significantly in the total population during the intervention while the relative abundance of Bifidobacterium longum and Bifidobacterium catenulatum decreased. Our results indicate that an increased intake of pea protein isolate affects the growth of certain beneficial bacterial strains and differentially influences markers related to gut inflammation in healthy individuals.", "doi": "10.1039/d5fo02653a", "pmid": "41481420", "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-03-05T09:09:35.428Z", "modified": "2026-03-05T09:09:35.867Z"}, {"entity": "publication", "iuid": "342a4ab7fa284801b476886e85244b3e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/342a4ab7fa284801b476886e85244b3e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/342a4ab7fa284801b476886e85244b3e"}}, "title": "NUP98 regulates orthoflavivirus replication through interaction with vRNA and can be targeted for antiviral purposes.", "authors": [{"family": "Peters", "given": "Marie B A", "initials": "MBA", "orcid": "0000-0001-8994-0864", "researcher": {"href": "https://publications.scilifelab.se/researcher/df4733590d054742b732c2028a8f5e8a.json"}}, {"family": "Lindqvist", "given": "Richard", "initials": "R"}, {"family": "Madhu", "given": "Priyanka", "initials": "P"}, {"family": "Lundmark", "given": "Richard", "initials": "R"}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y"}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK", "orcid": "0000-0001-6553-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/506b0e2b2d884f868df73c7663b9ffb7.json"}}], "type": "journal article", "published": "2026-01-22", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "54", "issue": "3", "issn-l": "0305-1048"}, "abstract": "The nuclear pore complex (NPC) is composed of multiple nucleoporins (NUPs) and enables the exchange of RNA and proteins between the nucleus and cytoplasm. NUP98 is one of the major components of the NPC, being involved in the RNA export pathway by interacting with several transport factors. Previous studies have suggested both proviral and antiviral functions of NUP98 in viral infection, yet little is known about its function in orthoflavivirus infection. In this study we show that NUP98 is a proviral cellular protein that is recruited to the cytoplasm during orthoflavivirus infection. We observe that NUP98 is found specifically in the vicinity of the replication vesicles during infections with tick-borne encephalitis virus, Japanese encephalitis virus, and yellow fever virus. Furthermore, using surface plasmon resonance, cross-link immunoprecipitation, and cross-link immunoprecipitation-sequencing we observe that the C-terminal domain of NUP98 directly interacts with a conserved site of the viral RNA (vRNA) in the E coding region promoting viral replication. We identified a peptide that binds to NUP98 that is antivirally active against several orthoflaviviruses by outcompeting the binding between NUP98 and vRNA, making NUP98 an attractive target for antiviral development.", "doi": "10.1093/nar/gkag027", "pmid": "41591840", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12839527"}, {"db": "pii", "key": "8442274"}], "notes": [], "created": "2026-02-27T08:03:17.950Z", "modified": "2026-06-01T11:13:48.642Z"}, {"entity": "publication", "iuid": "1e5708bc6c1c4c099e773f1d29e68641", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e5708bc6c1c4c099e773f1d29e68641.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e5708bc6c1c4c099e773f1d29e68641"}}, "title": "Anoctamin-2-specific T cells link Epstein-Barr virus to multiple sclerosis.", "authors": [{"family": "Thomas", "given": "Olivia G", "initials": "OG", "orcid": "0000-0002-2011-1344", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea07f812ffee4db893c6f98548563525.json"}}, {"family": "Rykaczewska", "given": "Urszula", "initials": "U"}, {"family": "Gale\u0161i\u0107", "given": "Marina", "initials": "M"}, {"family": "van der Burgt", "given": "Rianne T M", "initials": "RTM"}, {"family": "Hall\u00e9n", "given": "Nils", "initials": "N"}, {"family": "Ferro", "given": "Filippo", "initials": "F", "orcid": "0000-0002-6023-8227", "researcher": {"href": "https://publications.scilifelab.se/researcher/27810903638948feb4391fa537a7eda3.json"}}, {"family": "Bronge", "given": "Mattias", "initials": "M", "orcid": "0000-0002-1258-3982", "researcher": {"href": "https://publications.scilifelab.se/researcher/691b77352a57408896ef1fb486980ccd.json"}}, {"family": "Marti", "given": "Zoe", "initials": "Z"}, {"family": "Li", "given": "Yue", "initials": "Y"}, {"family": "Riqu\u00e9", "given": "Alexandra Hill", "initials": "AH"}, {"family": "Lin", "given": "Jianing", "initials": "J"}, {"family": "Krstic", "given": "Aleksa", "initials": "A"}, {"family": "Gromadzka", "given": "Alicja", "initials": "A"}, {"family": "Szonder", "given": "Andr\u00e1s Levente", "initials": "AL"}, {"family": "Sorini", "given": "Chiara", "initials": "C", "orcid": "0000-0002-6803-8377", "researcher": {"href": "https://publications.scilifelab.se/researcher/975173f37f144f06b236817e224de7f0.json"}}, {"family": "Reina-Campos", "given": "Mar\u00eda", "initials": "M"}, {"family": "Sun", "given": "Ting", "initials": "T", "orcid": "0000-0002-7104-7215", "researcher": {"href": "https://publications.scilifelab.se/researcher/521fca43267242fca06da0f5fc823e6a.json"}}, {"family": "Rubio Rodr\u00edguez-Kirby", "given": "Leslie A", "initials": "LA", "orcid": "0000-0003-4467-2661", "researcher": {"href": "https://publications.scilifelab.se/researcher/9790e215a63d40aa8fac497b537999f9.json"}}, {"family": "Dumral", "given": "\u00d6zge", "initials": "\u00d6", "orcid": "0000-0002-9980-2702", "researcher": {"href": "https://publications.scilifelab.se/researcher/8288edd47f70479e93e1fc441d486997.json"}}, {"family": "Berglund", "given": "Rasmus", "initials": "R"}, {"family": "Kakhki", "given": "Majid Pahlevan", "initials": "MP"}, {"family": "Adzemovic", "given": "Milena Z", "initials": "MZ"}, {"family": "Zeitelhofer", "given": "Manuel", "initials": "M"}, {"family": "Akpinar", "given": "Birce", "initials": "B"}, {"family": "Tengvall", "given": "Katarina", "initials": "K", "orcid": "0000-0003-0424-3571", "researcher": {"href": "https://publications.scilifelab.se/researcher/59b02aaaf03b4cd39150c3034888c81d.json"}}, {"family": "Nilsson", "given": "Ola B", "initials": "OB", "orcid": "0000-0002-7516-1760", "researcher": {"href": "https://publications.scilifelab.se/researcher/096ce3bf888b4ad395d53bb3c11f6946.json"}}, {"family": "Holmgren", "given": "Erik", "initials": "E", "orcid": "0000-0002-2656-1864", "researcher": {"href": "https://publications.scilifelab.se/researcher/6160949c45cf4daaab3991d051db5a16.json"}}, {"family": "Cucuzza", "given": "Chiara Starvaggi", "initials": "CS"}, {"family": "H\u00f6gelin", "given": "Klara Asplund", "initials": "KA"}, {"family": "Gafvelin", "given": "Guro", "initials": "G", "orcid": "0000-0003-1618-4011", "researcher": {"href": "https://publications.scilifelab.se/researcher/870294f4604744ccb212a3c299887ecc.json"}}, {"family": "Fink", "given": "Katharina", "initials": "K"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Khademi", "given": "Mohsen", "initials": "M", "orcid": "0000-0003-0801-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5446d6d754bc4c429d0e48ade419413c.json"}}, {"family": "Piehl", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8329-5219", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee04062fbee34836a4fa3f4d2e8076cd.json"}}, {"family": "Gr\u00e4slund", "given": "Torbj\u00f6rn", "initials": "T", "orcid": "0000-0002-5391-600X", "researcher": {"href": "https://publications.scilifelab.se/researcher/52adbc739e274652bbf877facf4f0959.json"}}, {"family": "Alfredsson", "given": "Lars", "initials": "L", "orcid": "0000-0003-1688-6697", "researcher": {"href": "https://publications.scilifelab.se/researcher/6df230614a8a448e8607e03480169658.json"}}, {"family": "Lund", "given": "Harald", "initials": "H", "orcid": "0000-0001-8046-0805", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fe4902c355449e4812008d4ad7a37e0.json"}}, {"family": "Uhl\u00e9n", "given": "Per", "initials": "P", "orcid": "0000-0003-1446-1062", "researcher": {"href": "https://publications.scilifelab.se/researcher/91c3e953634140b8974186ac0d7eac85.json"}}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Martin", "given": "Roland", "initials": "R"}, {"family": "Jagodic", "given": "Maja", "initials": "M", "orcid": "0000-0003-0756-889X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b651ef39c6b0436992e2305f425eba72.json"}}, {"family": "Gr\u00f6nlund", "given": "Hans", "initials": "H", "orcid": "0000-0003-4882-7624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e701613f60249b793f2def737168a05.json"}}, {"family": "Guerreiro-Cacais", "given": "Andr\u00e9 Ortlieb", "initials": "AO", "orcid": "0000-0002-4561-2823", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b824181455243b19f4aa145a4545870.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}], "type": "journal article", "published": "2026-01-22", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674", "volume": "189", "issue": "2", "pages": "585-602.e38"}, "abstract": "Epstein-Barr virus (EBV) infection constitutes a prerequisite for multiple sclerosis (MS) development, and cross-reactivity between EBV nuclear antigen 1 (EBNA1) and anoctamin-2 (ANO2) antibodies was previously demonstrated in persons with MS (pwMS). Here, we show that ANO2-specific CD4+ T cells are more frequent in pwMS. Immunization of SJL/J mice with ANO2 or EBNA1 led to cross-reactive CD4+ T cell and antibody responses. ANO2 pre-immunization led to exacerbated experimental autoimmune encephalomyelitis (EAE), an effect mediated by CD4+ T cells, as confirmed by adoptive transfer experiments. T cell clones with cross-reactivity to EBNA1 and ANO2 could be isolated from natalizumab-treated pwMS, and sequencing of EBNA1- and ANO2-specific T cell receptors (TCRs) revealed a significant repertoire overlap. We thus report the first mechanistic evidence that EBNA1 CD4+ T cells can target the MS autoantigen ANO2, thereby establishing a link between EBV infection and neuroinflammation.", "doi": "10.1016/j.cell.2025.12.032", "pmid": "41534529", "labels": {"Autoimmunity and Serology Profiling": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(25)01481-3"}], "notes": [], "created": "2026-01-15T20:23:02.729Z", "modified": "2026-03-24T09:17:16.086Z"}, {"entity": "publication", "iuid": "ffc3972ae9a14e7582201dd0cd2bba22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ffc3972ae9a14e7582201dd0cd2bba22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ffc3972ae9a14e7582201dd0cd2bba22"}}, "title": "Genetiska sl\u00e4ktskapsanalyser och individerna fr\u00e5n Riddarholmskyrkan (Magnus Ladul\u00e5s grav: om s\u00f6kandet i Riddarholmskyrkan)", "authors": [{"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}], "type": null, "published": "2026-01-21", "journal": {"title": null, "issn": "ISBN 9789170313936", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": null, "pmid": null, "labels": {"Ancient DNA": "Service"}, "xrefs": [], "notes": [], "created": "2026-01-20T09:33:18.868Z", "modified": "2026-01-25T08:37:46.888Z"}, {"entity": "publication", "iuid": "7113a2d0392946c48648bba31fb03588", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7113a2d0392946c48648bba31fb03588.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7113a2d0392946c48648bba31fb03588"}}, "title": "Integrative Epigenomic and Transcriptomic Profiling Define Malignancy- and Cluster-Specific Signatures in Pheochromocytomas and Paragangliomas", "authors": [{"family": "Tabebi", "given": "Mouna", "initials": "M", "orcid": "0000-0002-2873-161X", "researcher": {"href": "https://publications.scilifelab.se/researcher/285705c043f34b55826e7f33ab36a875.json"}}, {"family": "\u0141ysiak", "given": "Ma\u0142gorzata", "initials": "M", "orcid": "0000-0002-0244-759X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7f5d37e79764c31a5a0a421c34ed1a8.json"}}, {"family": "Gimm", "given": "Oliver", "initials": "O", "orcid": "0000-0002-0054-664X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9879641fb40042ae90ff034f4912a16d.json"}}, {"family": "S\u00f6derkvist", "given": "Peter", "initials": "P"}], "type": "journal-article", "published": "2026-01-20", "journal": {"title": "Cells", "issn": "2073-4409", "volume": "15", "issue": "2", "pages": "198", "issn-l": "2073-4409"}, "abstract": null, "doi": "10.3390/cells15020198", "pmid": null, "labels": {"Clinical Genomics": "Service", "Clinical Genomics Link\u00f6ping": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-01-26T09:31:12.459Z", "modified": "2026-01-26T09:32:30.489Z"}, {"entity": "publication", "iuid": "e351feeeda1348ee8f9fa630d927896b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e351feeeda1348ee8f9fa630d927896b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e351feeeda1348ee8f9fa630d927896b"}}, "title": "Results of Archaeological Research on Burials at St. George\u2019s Church in Gokhnari", "authors": [{"family": "Sulkhanishvili", "given": "David", "initials": "D"}, {"family": "Ioramashvili", "given": "Solomon", "initials": "S"}, {"family": "Mshvildadze", "given": "Madona", "initials": "M"}, {"family": "Goguadze", "given": "David", "initials": "D"}, {"family": "Burjanadze", "given": "Giorgi", "initials": "G"}], "type": null, "published": "2026-01-15", "journal": {"title": "Chronos", "issn": "ISSN 2667-9477", "issn-l": null, "volume": "6", "issue": null, "pages": "220\u2013246"}, "abstract": "The archaeological study of the cemetery located in the courtyard of St. George\u2019s Church in Gokhnari holds particular significance. This monument has repeatedly become the subject of discussion in scientific circles due to the relief compositions present on the tombstones. Until 2018, the main purpose of research was to explain the carving technology and determine their memorial attribution through observation of the subjects. As for archaeological excavations, no work had been conducted in this direction.\r\nThe article presents the results of archaeological investigations conducted by \u201cKhvamlis Amqari\u201d in 2018-2020. In the first season, the expedition conducted field surveys, small-scale cleaning work, and studied one of the burials existing in the church courtyard. It should be noted that the precise boundaries of the grave could not be determined during this phase. Consequently, it was hypothesised that the relief-carved tombstones might have marked a single, large collective burial. Accordingly, the purpose of the work planned for the second field season was to verify the expressed assumptions and many other hypotheses based on additional archaeological excavations and analysis of osteological material.\r\nIn 2020, archaeological excavations were conducted on two burials adjacent to the south-west of the grave uncovered during the first season. Excavation revealed that the burials had been reused multiple times for interments across different periods, which was confirmed by bone remains revealed at three distinct levels and the presence of stone-built burial constructions.\r\nTo assess the revealed archaeological picture, bone samples were submitted for radiocarbon dating at the Tandem Laboratory of Uppsala University and Ancient DNA analysis at Sweden\u2019s national SciLifeLab.\r\nThe radiocarbon results indicated that the earliest burial layer (lowest level) dates from the turn of the 10th-11th centuries, while the late (upper level) corresponds to the 12th-13th centuries. Notably, it was established that the disarticulated skeletal remains in the upper level predate the anatomically intact individual interred in an orderly manner in the so-called middle level. These findings further support scholarly claims regarding the contemporaneity of St. George\u2019s Church and the Gokhnari cemetery, dating to the transition from the 10th to 11th centuries.\r\nRegarding ancient DNA research, 13 samples were submitted for analysis to Sweden\u2019s national SciLifeLab. For most of them, Y chromosome and mitochondrial DNA haplogroups were deciphered, enabling us to determine the sex of the individuals and to infer aspects of their ethnic or regional background.\r\nThe scale of the archaeological field work and the results of laboratory data of osteological material at our disposal are, of course, insufficient for constructing a comprehensive understanding or drawing definitive conclusions. Accordingly, continued multidisciplinary research is essential for the full investigation and interpretation of the cemetery.", "doi": null, "pmid": null, "labels": {"Ancient DNA": "Service"}, "xrefs": [], "notes": [], "created": "2026-01-15T13:42:07.368Z", "modified": "2026-01-15T13:42:07.369Z"}, {"entity": "publication", "iuid": "8cb122c7905e4043bd3f13414014d2fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8cb122c7905e4043bd3f13414014d2fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8cb122c7905e4043bd3f13414014d2fe"}}, "title": "The long noncoding RNA VIM-AS1 and nucleoporin Nup358/RanBP2 regulate SMAD nuclear accumulation during TGF-\u03b2 signaling.", "authors": [{"family": "Rodrigues-Junior", "given": "Dorival Mendes", "initials": "DM", "orcid": "0000-0002-8861-9240", "researcher": {"href": "https://publications.scilifelab.se/researcher/3334d6f77c1f42c2b10fd3e9bef23efb.json"}}, {"family": "Ali", "given": "Mohamad Moustafa", "initials": "MM"}, {"family": "Itoh", "given": "Yuka", "initials": "Y"}, {"family": "Ferreira", "given": "Mafalda Sousa", "initials": "MS"}, {"family": "Heldin", "given": "Johan", "initials": "J", "orcid": "0000-0002-0915-5303", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8a546798d014cd3a44537ae5db9f889.json"}}, {"family": "Fu", "given": "Hao", "initials": "H"}, {"family": "Hoelz", "given": "Andr\u00e9", "initials": "A"}, {"family": "Heldin", "given": "Carl-Henrik", "initials": "CH"}, {"family": "Moustakas", "given": "Aristidis", "initials": "A", "orcid": "0000-0001-9131-3827", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c1626d991f3485e81232db174537e6d.json"}}], "type": "journal article", "published": "2026-01-14", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "54", "issue": "2", "issn-l": "0305-1048"}, "abstract": "The transforming growth factor \u03b2 (TGF-\u03b2) pathway is a developmental signaling network that regulates tissue homeostasis and malfunctions in human diseases, including cancer. TGF-\u03b2 signals via two receptors, which activate SMAD and alternative signaling pathways. We show that TGF-\u03b2 induces the expression of the mammalian long noncoding RNA (lncRNA) VIM-AS1 (Vimentin antisense RNA1) variant-2 (v.2) via a transcriptional SMAD-GATA6-SPI1 complex. VIM-AS1 v.1 and v.2 localize in different cell compartments, including the nuclear border. Unbiased whole transcriptomic analysis and functional gain and loss of function assays establish that VIM-AS1 v.2 enhances TGF-\u03b2 signaling. Mechanistically, VIM-AS1 v.2 interacts with the nucleoporin Nup358/RanBP2, contributing to the binding of Nup358/RanBP2 to SMAD2/3 and enhancing SMAD nuclear accumulation. In the context of cancer biology, VIM-AS1 did not affect the antiproliferative actions of TGF-\u03b2, yet had an impact on the epithelial-mesenchymal transition gene program, and increased the invasion and motility of tumor cells, whereas its silencing sensitized cancer cells to chemotherapeutic agents. The molecular mechanism highlights how a lncRNA can modulate the nuclear pore's capacity to import SMAD complexes, by facilitating their capture by Nup358/RanBP2 and thereby enhancing nuclear accumulation of SMADs with distinct isoform composition, thus promoting selectively TGF-\u03b2 signaling responses.", "doi": "10.1093/nar/gkaf1526", "pmid": "41556346", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12817083"}, {"db": "pii", "key": "8431143"}], "notes": [], "created": "2026-06-01T11:10:58.548Z", "modified": "2026-06-01T11:10:58.802Z"}, {"entity": "publication", "iuid": "996018f364704a1abe996db7068a45d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/996018f364704a1abe996db7068a45d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/996018f364704a1abe996db7068a45d8"}}, "title": "Phylum-wide propionate degradation and its potential connection to poly-gamma-glutamate biosynthesis in Candidatus Cloacimonadota phylum.", "authors": [{"family": "Calusinska", "given": "Magdalena", "initials": "M", "orcid": "0000-0003-2270-2217", "researcher": {"href": "https://publications.scilifelab.se/researcher/f184fc41010f4815b8ba4a2203bdab1b.json"}}, {"family": "Herold", "given": "Malte", "initials": "M", "orcid": "0000-0003-2627-0159", "researcher": {"href": "https://publications.scilifelab.se/researcher/70759c28794141fbb123901947534ec4.json"}}, {"family": "Klimek", "given": "Dominika", "initials": "D", "orcid": "0000-0002-6713-8333", "researcher": {"href": "https://publications.scilifelab.se/researcher/39f020f1807c426c988f2ba6a8d6ac2e.json"}}, {"family": "Bertucci", "given": "Marie", "initials": "M", "orcid": "0009-0003-5131-0746", "researcher": {"href": "https://publications.scilifelab.se/researcher/139ca2da31b34ebe9104aa4f370a937b.json"}}, {"family": "Lemaigre", "given": "S\u00e9bastien", "initials": "S", "orcid": "0000-0002-3204-293X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfe56744791c4ef1a59a7eb187ded69f.json"}}, {"family": "Cambier", "given": "S\u00e9bastien", "initials": "S"}, {"family": "Zorzan", "given": "Simone", "initials": "S"}, {"family": "Leclercq", "given": "C\u00e9line", "initials": "C", "orcid": "0000-0003-0565-4591", "researcher": {"href": "https://publications.scilifelab.se/researcher/13f9babdf8e24b7098ab25c45af2c06a.json"}}, {"family": "Dolfing", "given": "Jan", "initials": "J", "orcid": "0000-0002-7220-530X", "researcher": {"href": "https://publications.scilifelab.se/researcher/13c979337df149d78d462df170b54296.json"}}, {"family": "Westerholm", "given": "Maria", "initials": "M", "orcid": "0000-0003-2150-8762", "researcher": {"href": "https://publications.scilifelab.se/researcher/773b448833474db9aef273531d590892.json"}}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B", "orcid": "0000-0002-0030-7710", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c1cb5bfdb1a4ceaa551d5908b54e062.json"}}, {"family": "Nasirzadeh", "given": "Leila", "initials": "L", "orcid": "0000-0003-0282-1227", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9465e8d872740a083579657d96bb431.json"}}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A", "orcid": "0000-0003-0038-553X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f81992bc8ed48318f8197fc8caabb4f.json"}}, {"family": "Wilmes", "given": "Paul", "initials": "P", "orcid": "0000-0002-6478-2924", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0fa4b91d7384fda991fcda7c3df41be.json"}}, {"family": "Delfosse", "given": "Philippe", "initials": "P", "orcid": "0009-0003-9371-209X", "researcher": {"href": "https://publications.scilifelab.se/researcher/85d6d628631f4012941393e3b7f03a64.json"}}, {"family": "Goux", "given": "Xavier", "initials": "X", "orcid": "0000-0002-0815-2194", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ee58ca55da3480b864a0a26f15649ae.json"}}], "type": "journal article", "published": "2026-01-14", "journal": {"title": "ISME J", "issn": "1751-7370", "volume": "20", "issue": "1", "issn-l": "1751-7362"}, "abstract": "The candidate phylum Cloacimonadota is frequently detected in anoxic environments such as anaerobic digestion (AD) reactors, hydrothermal vents, and deep-sea sediments, yet its metabolism remains poorly understood. Metagenomic evidence suggests capacities for amino acid fermentation, carbohydrate degradation, as well as a potential role in syntrophic propionate oxidation (SPO), a key bottleneck in AD. However, a complete methylmalonyl-CoA (mmc) pathway, central to SPO, has not been previously identified in Cloacimonadota genomes. Here, we report results from an acidified lab-scale anaerobic baffled reactor fed with sugar beet pulp, where an increase in the relative abundance of Cloacimonadota correlated with recovery of methanogenesis, resulting in increased methane content in the produced biogas. Metagenomic and metatranscriptomic analyses enabled metabolic reconstruction of the dominant Cloacimonadota operational taxonomic unit (OTU). Furthermore, using a curated database of 204 genome-resolved Cloacimonadota species, we characterized the phylum-level metabolic potential. Comparative genomics revealed alternative proteins, including 2-oxoglutarate:ferredoxin oxidoreductase and aspartate aminotransferase, likely to substitute for missing enzymes in the classical mmc pathway. These proteins were widely distributed and highly conserved across the analyzed Cloacimonadota genomes, suggesting that this variant of the SPO pathway could represent a phylum-specific trait. Moreover, we hypothesize that these alternative pathway steps may link propionate metabolism to protein degradation and poly-\u03b3-glutamate biosynthesis. Network analysis identified the methanogenic archaeon Methanothrix as a potential syntrophic partner, an interaction further supported by propionate-fed enrichment cultures showing co-occurrence of Cloacimonadota and Methanothrix species. Our study sheds light on the Cloacimonadota metabolism, advancing our understanding of their ecological roles and potential for biotechnological applications.", "doi": "10.1093/ismejo/wrag055", "pmid": "41848058", "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics Link\u00f6ping": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC13082233"}, {"db": "pii", "key": "8527530"}], "notes": [], "created": "2026-06-09T06:06:08.699Z", "modified": "2026-06-09T06:06:09.571Z"}, {"entity": "publication", "iuid": "0b5071faf9e94295890d2321eea1b81a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b5071faf9e94295890d2321eea1b81a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b5071faf9e94295890d2321eea1b81a"}}, "title": "Metabolic interactions between bacterial co-isolates from catheter-associated urinary tract infections", "authors": [{"family": "Sokol", "given": "Dmytro", "initials": "D"}, {"family": "Rzhepishevska", "given": "Olena", "initials": "O", "orcid": "0000-0002-7912-7447", "researcher": {"href": "https://publications.scilifelab.se/researcher/53216ecce7934eb3a4beedb82f318fc5.json"}}, {"family": "Marynova", "given": "Iryna", "initials": "I"}, {"family": "Monsen", "given": "Tor", "initials": "T"}, {"family": "Antti", "given": "Henrik", "initials": "H"}, {"family": "Ramstedt", "given": "Madeleine", "initials": "M", "orcid": "0000-0003-2646-8501", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0fb139ad40341fd85e4ba6fe39eb7fe.json"}}], "type": "journal-article", "published": "2026-01-14", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "pages": "2061", "issn-l": "2045-2322"}, "abstract": "Catheter-associated urinary tract infections (CAUTI) are complex infections often involving multi-species bacteria. Escherichia coli is frequently an early coloniser. Subsequent colonisation by Pseudomonas aeruginosa and coexistence mechanisms between the two strains within urethral catheters is not yet fully understood. In this study, metabolic adaptations between co-isolated clinical E. coli and P. aeruginosa strains were investigated. It was found that P. aeruginosa outgrew E. coli in artificial urine medium (AUM), whereas E. coli dominated in culture broth such as Iso-sensitest. No evidence of direct antagonism was observed. Metabolite analyses revealed distinct metabolite patterns indicating cross-feeding and metabolic adaptations. In AUM, stress-response metabolites were elevated. Additionally, E. coli appeared to experience Fe-limitation in AUM, while the same was not observed for P. aeruginosa. The results highlight the influence of nutrient conditions on processes within mixed biofilms.\n\nThe online version contains supplementary material available at 10.1038/s41598-025-33855-1.", "doi": "10.1038/s41598-025-33855-1", "pmid": "41535363", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12808099"}, {"db": "pii", "key": "10.1038/s41598-025-33855-1"}], "notes": [], "created": "2026-02-23T09:04:21.178Z", "modified": "2026-03-24T09:14:47.860Z"}, {"entity": "publication", "iuid": "4f13015ae8624d2280a97f539bbf89b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f13015ae8624d2280a97f539bbf89b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f13015ae8624d2280a97f539bbf89b0"}}, "title": "Dealing with phosphorus deficiency: contrasting strategies in marine phytoplankton and bacteria", "authors": [{"family": "Delgadillo-Nu\u00f1o", "given": "Erick", "initials": "E"}, {"family": "Teira", "given": "Eva", "initials": "E", "orcid": "0000-0002-4333-0101", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ed7047ae09241a182466fee66736dbd.json"}}, {"family": "Fern\u00e1ndez", "given": "Emilio", "initials": "E", "orcid": "0000-0001-7985-0814", "researcher": {"href": "https://publications.scilifelab.se/researcher/748dd6833e474966b5c7b79ef52dd1c7.json"}}, {"family": "Justel-D\u00edez", "given": "Maider", "initials": "M"}, {"family": "Di Leo", "given": "Danilo", "initials": "D"}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Mart\u00ednez-Garc\u00eda", "given": "Sandra", "initials": "S", "orcid": "0000-0002-5476-7499", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc1a03d6cd414b748807788a0c8e11fb.json"}}], "type": "journal-article", "published": "2026-01-14", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "6", "issue": "1", "pages": "ycag035", "issn-l": null}, "abstract": "Phosphorus (P) and nitrogen (N) are essential nutrients for microbial growth, playing crucial roles in regulating the biological productivity of marine ecosystems. Over the last decades, the relatively higher increase in anthropogenic N compared to P inputs is causing a continuous increase in the N:P supply ratio to the global biosphere. The high N:P ratio of riverine discharge may seasonally cause P limitation in estuaries and river-dominated continental shelf waters. We conducted a mesocosm experiment simulating a P-deplete and a P-replete riverine discharge to coastal waters in NW Spain to assess the functional response of marine microplankton using a metatranscriptomic approach. By examining the expression of 40 well-documented genes related to P-metabolism in prokaryotic and eukaryotic gene expression, we uncovered pronounced changes in microbial P-metabolism induced by riverine N:P ratio in this productive system. Remarkably, heterotrophic bacteria and eukaryotic phytoplankton exhibited contrasting phosphate metabolism strategies in response to P deficiency, with the former mostly expressing genes coding for high-affinity transporters and the latter mostly transcribing genes related with low-affinity transporters. Our results also highlight distinct regulatory and adaptive mechanisms across different members of the prokaryotic and eukaryotic communities when exposed to varying P concentrations. Our findings shed light on the broader ecological and functional roles of these genes in nutrient cycling within aquatic ecosystems, with potential application for the design of diagnostic tools for P status in coastal productive systems.", "doi": "10.1093/ismeco/ycag035", "pmid": "41835132", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12981677"}, {"db": "pii", "key": "ycag035"}], "notes": [], "created": "2026-03-23T13:43:18.783Z", "modified": "2026-03-24T09:16:03.978Z"}, {"entity": "publication", "iuid": "956e57bde6744efc807a93e14f61238f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/956e57bde6744efc807a93e14f61238f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/956e57bde6744efc807a93e14f61238f"}}, "title": "Cefiderocol resistance genes identified in environmental samples using functional metagenomics.", "authors": [{"family": "Gschwind", "given": "Remi", "initials": "R", "orcid": "0000-0001-7741-9764", "researcher": {"href": "https://publications.scilifelab.se/researcher/d15bb307008d40968a53a320eb2f4571.json"}}, {"family": "Bonnet", "given": "Mehdi", "initials": "M"}, {"family": "Abramova", "given": "Anna", "initials": "A"}, {"family": "Jarqu\u00edn-D\u00edaz", "given": "Victor Hugo", "initials": "VH"}, {"family": "Wenne", "given": "Marcus", "initials": "M"}, {"family": "L\u00f6ber", "given": "Ulrike", "initials": "U", "orcid": "0000-0001-7468-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/7180811b734042c0b3b8fb3f2ee03e5e.json"}}, {"family": "Godron", "given": "Nicolas", "initials": "N"}, {"family": "Kampouris", "given": "Ioannis D", "initials": "ID"}, {"family": "Tskhay", "given": "Faina", "initials": "F"}, {"family": "Nahid", "given": "Fouzia", "initials": "F"}, {"family": "Debroucker", "given": "Chlo\u00e9", "initials": "C"}, {"family": "Bui-Hai", "given": "Maximilien", "initials": "M"}, {"family": "El Aiba", "given": "In\u00e8s", "initials": "I"}, {"family": "Kl\u00fcmper", "given": "Uli", "initials": "U", "orcid": "0000-0002-4169-6548", "researcher": {"href": "https://publications.scilifelab.se/researcher/effd67c0296c4d539c41292224ba310a.json"}}, {"family": "Berendonk", "given": "Thomas U", "initials": "TU"}, {"family": "Forslund-Startceva", "given": "Sofia K", "initials": "SK"}, {"family": "Zahra", "given": "Rabaab", "initials": "R"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications.scilifelab.se/researcher/267ff77d11e04a30bacdd0ae7492bea8.json"}}, {"family": "Rupp\u00e9", "given": "Etienne", "initials": "E"}], "type": "journal article", "published": "2026-01-14", "journal": {"title": "ISME J", "issn": "1751-7370", "volume": "20", "issue": "1", "issn-l": "1751-7362"}, "abstract": "Antibiotic resistance poses a global public health threat, which can originate from the transfer of environmental antibiotic resistance genes to pathogenic bacteria, as highlighted by the \"One Health\" framework. Cefiderocol is a siderophore cephalosporin recently introduced in clinical practice which displays a \"Trojan Horse\" mechanism, utilizing bacterial iron transportation systems for cell entry. Although it is only used as a last-line antibiotic, resistance has already been observed in clinical isolates. Yet, cefiderocol resistance genes are difficult to monitor as resistance mechanisms remain mostly undescribed in antibiotic resistance gene databases and therefore uncharacterized in the environment. To address this critical gap, we applied functional metagenomics to diverse environmental samples (wastewater, freshwater, and soil) from France, Germany, Sweden, and Pakistan. Four antibiotic resistant genes were identified as responsible for increased cefiderocol minimum inhibitory concentrations to clinically-relevant levels (ranging from 1 to 4 mg/l), including \ua7b5-lactamases (VEB-3, OXA-372 homolog, and YbxI homolog) and a partial penicillin-binding protein homolog. None of these genes had been previously reported as a cefiderocol resistance gene. Three out of four had their closest homologs in pathogenic bacteria. The blaVEB-3 gene was associated with a mobile genetic element and distributed across all wastewater metagenomes analyzed in this study. We therefore highlight the critical need for functional metagenomics, to characterize previously uncharacterized last-line antibiotic resistance mechanisms which will be used to enrich antibiotic resistance gene databases and thereby improving antibiotic resistance surveillance in all One Health compartments.", "doi": "10.1093/ismejo/wrag010", "pmid": "41603547", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12915585"}, {"db": "pii", "key": "8443128"}], "notes": [], "created": "2026-06-01T11:11:00.738Z", "modified": "2026-06-01T11:11:00.948Z"}, {"entity": "publication", "iuid": "458be5facf88424ab597423133f064c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/458be5facf88424ab597423133f064c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/458be5facf88424ab597423133f064c6"}}, "title": "Active methylotrophic methanogenesis by a microbial consortium enriched from a terrestrial meteorite impact crater.", "authors": [{"family": "van Dam", "given": "Femke", "initials": "F", "orcid": "0000-0002-5526-5044", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6869844c377483abb30634c303da5fb.json"}}, {"family": "Westmeijer", "given": "George", "initials": "G"}, {"family": "Rezaei Somee", "given": "Maryam", "initials": "M"}, {"family": "Ketzer", "given": "Marcelo", "initials": "M"}, {"family": "Kiet\u00e4v\u00e4inen", "given": "Riikka", "initials": "R"}, {"family": "Ono", "given": "Shuhei", "initials": "S"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "McIntosh", "given": "Jennifer C", "initials": "JC"}, {"family": "Dopson", "given": "Mark", "initials": "M"}, {"family": "Drake", "given": "Henrik", "initials": "H", "orcid": "0000-0001-7230-6509", "researcher": {"href": "https://publications.scilifelab.se/researcher/d25c4627832844518873bb13021a2ef0.json"}}], "type": "journal article", "published": "2026-01-14", "journal": {"title": "MBio", "issn": "2150-7511", "volume": "17", "issue": "1", "pages": "e0301725", "issn-l": null}, "abstract": "Microbial methane generation (methanogenesis) is an important metabolic process in the terrestrial deep biosphere and is an analog to early Earth as it is proposed to be one of the most ancient metabolisms on Earth. Signs of methanogenesis in meteorite impact craters are of particular interest in this respect as these settings are proposed hot spots for deep microbial colonization of the upper crust. Yet, reports of active deep rock-hosted methanogenesis are scarce, particularly for methylotrophic methanogenesis, while reports from terrestrial meteorite impact craters are completely lacking. Here, we used indigenous communities in cultures enriched from 400-m deep fluids to confirm and characterize active methane production from several carbon donors, including indigenous oil, in a terrestrial impact crater at Siljan, Sweden. Metagenomic and metatranscriptomic data of the methane-producing cultures revealed a consortium dominated by Acetobacterium sp. KB-1 and Candidatus Methanogranum gryphiswaldense, mediating methanogenesis solely via the methyl-reduction pathway, and resulting in a \u03b413Cmethanol-methane isotope enrichment of up to 98.6\u2030. These results provide insights into methylotrophic methanogenesis in deep subsurface environments in general, and in particular in fractured meteorite impact structures.IMPORTANCEThis study revealed that microbes enriched from groundwater in a 380-m deep borehole within the Siljan meteorite impact crater in Sweden were capable of producing methane, a key greenhouse gas. This is especially significant because it is the first proof of active methanogens in an impact crater and showing a specific pathway of methane production-methylotrophic methanogenesis-is present in the deep terrestrial subsurface, an environment that is typically hard to study. These findings shed light on life in extreme conditions on Earth and show that meteorite craters can be biological hotspots, rich with ancient life processes.", "doi": "10.1128/mbio.03017-25", "pmid": "41288100", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12802149"}], "notes": [], "created": "2026-06-01T11:13:52.580Z", "modified": "2026-06-01T11:13:52.612Z"}, {"entity": "publication", "iuid": "7754d49a002a45ea96c366c1cf61c7fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7754d49a002a45ea96c366c1cf61c7fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7754d49a002a45ea96c366c1cf61c7fb"}}, "title": "A combinatorial transcription factor screening platform for immune cell reprogramming.", "authors": [{"family": "Kurochkin", "given": "Ilia", "initials": "I", "orcid": "0000-0003-3100-0903", "researcher": {"href": "https://publications.scilifelab.se/researcher/215e3195c7a943578f6fc51e367fb3af.json"}}, {"family": "Altman", "given": "Abigail R", "initials": "AR"}, {"family": "Caiado", "given": "In\u00eas", "initials": "I", "orcid": "0000-0001-5015-2705", "researcher": {"href": "https://publications.scilifelab.se/researcher/cef853aaa15943f7ac12a225fc590d84.json"}}, {"family": "P\u00e9rtiga-Cabral", "given": "Diogo", "initials": "D"}, {"family": "Halitzki", "given": "Evelyn", "initials": "E"}, {"family": "Minaeva", "given": "Mariia", "initials": "M"}, {"family": "Zimmermannov\u00e1", "given": "Olga", "initials": "O", "orcid": "0000-0002-5706-8124", "researcher": {"href": "https://publications.scilifelab.se/researcher/19ffa427694b45e4800bf54cc457bd3d.json"}}, {"family": "Henriques-Oliveira", "given": "Lu\u00eds", "initials": "L"}, {"family": "Klein", "given": "Dominik", "initials": "D"}, {"family": "Nair", "given": "Malavika", "initials": "M"}, {"family": "Oliveira", "given": "Daniel", "initials": "D", "orcid": "0000-0003-0622-2934", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a7d211d1bfb41c28c667db817d8a7fb.json"}}, {"family": "Cajal", "given": "Laura Rabanal", "initials": "LR"}, {"family": "Knittel", "given": "Ramin", "initials": "R"}, {"family": "Feick", "given": "Cora", "initials": "C"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M", "orcid": "0000-0001-5469-8940", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0308e6d9c534033b431d2552cfe2af6.json"}}, {"family": "Martin", "given": "Marcel", "initials": "M"}, {"family": "Cirovic", "given": "Branko", "initials": "B"}, {"family": "Pires", "given": "Cristiana F", "initials": "CF", "orcid": "0000-0003-2985-6323", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dde1908f0e8470dbfac54d3202e0515.json"}}, {"family": "Rosa", "given": "Fabio F", "initials": "FF", "orcid": "0000-0002-7714-5852", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d6242040a284b6c9a2ee37f773e9adb.json"}}, {"family": "Sitnicka", "given": "Ewa", "initials": "E"}, {"family": "Theis", "given": "Fabian J", "initials": "FJ", "orcid": "0000-0002-2419-1943", "researcher": {"href": "https://publications.scilifelab.se/researcher/15139e290953411590201d9bb402da1f.json"}}, {"family": "Pereira", "given": "Carlos-Filipe", "initials": "CF", "orcid": "0000-0002-9724-1382", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b298bb485b744fdb87f51ad579d0a79.json"}}], "type": "journal article", "published": "2026-01-14", "journal": {"title": "Cell Syst", "issn": "2639-5460", "pages": "101457", "issn-l": "2405-4712"}, "abstract": "Direct reprogramming of immune cells holds promise for immunotherapy but is constrained by limited knowledge of transcription factor (TF) networks. Here, we developed REPROcode, a combinatorial single-cell screening platform to identify TF combinations for immune cell reprogramming. We first validated REPROcode by inducing type-1 conventional dendritic cells (cDC1s) with multiplexed sets of 9, 22, and 42 factors. With cDC1-enriched TFs, REPROcode enabled identification of optimal TF stoichiometry, fidelity enhancers, and regulators of cDC1 states. We then constructed an arrayed lentiviral library of 408 barcoded immune TFs to explore broader reprogramming capacity. Screening 48 TFs enriched in dendritic cell subsets yielded myeloid and lymphoid phenotypes and enabled the construction of a TF hierarchy map to guide immune reprogramming. Finally, we validated REPROcode's discovery power by inducing natural killer (NK)-like cells. This study deepens our understanding of immune transcriptional control and provides a versatile toolbox for engineering immune cells to advance immunotherapy.", "doi": "10.1016/j.cels.2025.101457", "pmid": "41539305", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2405-4712(25)00290-X"}], "notes": [], "created": "2026-01-15T13:40:34.207Z", "modified": "2026-01-20T07:55:14.966Z"}, {"entity": "publication", "iuid": "c586da7cc0cf4911a6d5d9d9ce6be426", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c586da7cc0cf4911a6d5d9d9ce6be426.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c586da7cc0cf4911a6d5d9d9ce6be426"}}, "title": "Structural basis for late maturation steps of mitochondrial respiratory chain complex IV within the human respirasome.", "authors": [{"family": "Nguyen", "given": "Minh Duc", "initials": "MD", "orcid": "0000-0003-2945-9707", "researcher": {"href": "https://publications.scilifelab.se/researcher/c66f3b3aa7c147558c0c1a7a1b079d09.json"}}, {"family": "Sierra-Magro", "given": "Ana", "initials": "A", "orcid": "0000-0002-2810-8377", "researcher": {"href": "https://publications.scilifelab.se/researcher/eae822e08d3443fd9d7addb3616553c5.json"}}, {"family": "Singh", "given": "Vivek", "initials": "V", "orcid": "0000-0003-4656-3362", "researcher": {"href": "https://publications.scilifelab.se/researcher/0576b8ffc93d42f6b47d9d0d7d01bbd0.json"}}, {"family": "Khawaja", "given": "Anas", "initials": "A", "orcid": "0000-0002-9721-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/a699763ef41f49d6b558e208fedc3db8.json"}}, {"family": "Tim\u00f3n-G\u00f3mez", "given": "Alba", "initials": "A", "orcid": "0000-0001-9811-8557", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1bd3e28e3214dd58dc5eddc21d469b3.json"}}, {"family": "Barrientos", "given": "Antoni", "initials": "A", "orcid": "0000-0001-9018-3231", "researcher": {"href": "https://publications.scilifelab.se/researcher/07a9331fc2df454c9c6e288f70c8c976.json"}}, {"family": "Rorbach", "given": "Joanna", "initials": "J", "orcid": "0000-0002-2891-2840", "researcher": {"href": "https://publications.scilifelab.se/researcher/a069374613a7403b818ce7ca400f3627.json"}}], "type": "journal article", "published": "2026-01-10", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723"}, "abstract": "The mitochondrial respiratory chain comprises four multimeric complexes (CI-CIV) that drive oxidative phosphorylation by transferring electrons to oxygen and generating the proton gradient required for ATP synthesis. These complexes can associate into supercomplexes (SCs), such as the CI + CIII\u2082 + CIV respirasome, but how SCs form, by joining preassembled complexes or by engaging partially assembled intermediates, remains unresolved. Here, we use cryo-electron microscopy to determine high-resolution structures of native human CI + CIII\u2082 + CIV late-assembly intermediates. Together with biochemical analyses, these structures show that respirasome biogenesis concludes with the final maturation of CIV while it is associated with fully assembled CI and CIII\u2082. We identify HIGD2A as a placeholder factor within isolated and supercomplexed CIV that is replaced by subunit NDUFA4 during the last step of CIV and respirasome assembly. This mechanism suggests that placeholders such as HIGD2A act as molecular timers, preventing premature incorporation of NDUFA4 or its isoforms and ensuring the orderly progression of pre-SC particles into functional respirasomes. Since defects in CIV assembly, including NDUFA4 deficiencies, cause severe encephalomyopathies and neurodegenerative disorders, understanding the molecular architecture and assembly pathways of isolated and supercomplexed CIV offers insight into the pathogenic mechanisms underlying these conditions.", "doi": "10.1038/s41467-025-68274-3", "pmid": "41519940", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-025-68274-3"}], "notes": [], "created": "2026-01-25T10:08:32.804Z", "modified": "2026-01-25T10:08:33.699Z"}, {"entity": "publication", "iuid": "a51aace6039f4479909a5aafa46886fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a51aace6039f4479909a5aafa46886fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a51aace6039f4479909a5aafa46886fb"}}, "title": "Proteomic and Lipidomic Profiling of Immune Cell\u2010Derived Subpopulations of Extracellular Vesicles", "authors": [{"family": "Lischnig", "given": "Anna", "initials": "A", "orcid": "0000-0001-7742-6905", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c26ce2f15ee46a9b19d59ebd3af7b96.json"}}, {"family": "Karimi", "given": "Nasibeh", "initials": "N", "orcid": "0000-0003-1499-6876", "researcher": {"href": "https://publications.scilifelab.se/researcher/14632eec875c42038aa0b6983e0ec107.json"}}, {"family": "Larsson", "given": "Per", "initials": "P", "orcid": "0000-0002-0456-8192", "researcher": {"href": "https://publications.scilifelab.se/researcher/d642894225474576b4a7c055fa7cb963.json"}}, {"family": "Ekstr\u00f6m", "given": "Karin", "initials": "K", "orcid": "0000-0001-7808-4572", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1922e7379bb4a5ca81b7db180a2d694.json"}}, {"family": "Crescitelli", "given": "Rossella", "initials": "R", "orcid": "0000-0002-1714-3169", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d4b955f26ca4a679deb090e30d0ccf1.json"}}, {"family": "Olin", "given": "Anna\u2010Carin", "initials": "A"}, {"family": "L\u00e4sser", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-1279-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/e14e17d2cdb24a9f93991d83811c78b9.json"}}], "type": "journal-article", "published": "2026-01-10", "journal": {"title": "Proteomics", "issn": "1615-9853", "issn-l": null, "volume": null, "issue": null, "pages": "e70096"}, "abstract": "Extracellular vesicles (EVs) are heterogeneous and play important roles in intercellular communication, contributing to physiological and pathological processes. Since few markers currently exist to differentiate subtypes of EVs, this study aimed to determine proteomic and lipidomic differences among four EV subpopulations. Large and small EVs (L-EVs and S-EVs) were isolated from human mast cells (HMC-1) and monocytes (THP-1) by differential ultracentrifugation and then further separated by density cushions into two different densities [low-density (LD) and high-density (HD)]. L-EVs were pelleted at 16,500 \u00d7 g, and S-EVs were pelleted at 118,000 \u00d7 g. LD EVs were collected at 1.079-1.146 g/mL, while HD EVs were collected at 1.146-1.185 g/mL. The morphology, size and yield of EVs were determined by TEM and western blot. The proteome and lipidome of the EV subpopulations were determined with mass spectrometry. A total of 5364 proteins were quantified, and L-EVs LD were enriched in mitochondrial proteins such as TIMM/TOMM and MICOS proteins, while L-EVs HD were enriched in cytoskeleton- and cytokinesis-associated proteins, such as KIF proteins. S-EVs LD were enriched in tetraspanins, ADAM10 and ESCRT machinery proteins, while S-EVs HD were enriched in proteins commonly viewed as contaminants, such as histones, complement factors and collagen. Proteins involved in membrane trafficking between the plasma membrane and organelles, such as adaptor protein complexes, the conserved oligomeric Golgi complex, the trafficking protein particle complex, sortin-nexins, TBC1 domain proteins and coatomer subunits, were expressed at similar levels across all EV subtypes. Furthermore, 107 lipids were quantified, and phosphatidylethanolamine (PE) was less abundant in L-EVs LD as compared to the other EV subtypes, while ceramides were enriched in L-EVs as compared to S-EVs.This study demonstrates that there is a core proteome and lipidome that is similar across all four EV subtypes, but importantly, it also shows that a portion of the proteome and lipidome differs in EV subpopulations separated based on size and density. We suggest that these could be important markers in future EV studies and that they may reflect a different biogenesis and EV function.", "doi": "10.1002/pmic.70096", "pmid": "41518059", "labels": {"Glycoproteomics and MS Proteomics": "Service", "Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2026-01-27T13:33:15.036Z", "modified": "2026-02-11T12:53:10.765Z"}, {"entity": "publication", "iuid": "1ff43766eb154a0eaf667914e8c3c386", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ff43766eb154a0eaf667914e8c3c386.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ff43766eb154a0eaf667914e8c3c386"}}, "title": "Marine-Inspired Antimicrobial Peptides Disrupt Gene Expression at the DNA Level.", "authors": [{"family": "Beyer", "given": "Luisa I", "initials": "LI"}, {"family": "Thoma", "given": "Johannes", "initials": "J", "orcid": "0000-0003-3584-8274", "researcher": {"href": "https://publications.scilifelab.se/researcher/98d27ad4d2224fbaa840469f85a596e4.json"}}, {"family": "Acha Alarcon", "given": "Leonarda", "initials": "L", "orcid": "0000-0002-9453-7479", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fa254340a5b4ec39809654b54fd3481.json"}}, {"family": "Unksov", "given": "Ivan N", "initials": "IN"}, {"family": "Karlsson", "given": "Roger", "initials": "R"}, {"family": "Inda-D\u00edaz", "given": "Juan S", "initials": "JS"}, {"family": "Tietze", "given": "Alesia A", "initials": "AA", "orcid": "0000-0002-9281-548X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c9c55ec11d84630a4b4472cd21ef96b.json"}}], "type": "journal article", "published": "2026-01-09", "journal": {"title": "ACS Infect Dis", "issn": "2373-8227", "volume": "12", "issue": "1", "pages": "447-459", "issn-l": null}, "abstract": "Genome mining of Streptomyces sp. H-KF8 combined with sequence engineering yielded two serum-stable, noncytotoxic, nonlytic antimicrobial peptides, L3 and L3-K. Initial studies in uropathogenic Escherichia coli suggested membrane effects and nucleoid relaxation, prompting a comprehensive investigation of their mode of action. In this study tandem mass tag (TMT)-based quantitative proteomics revealed extensive proteome remodeling, with 175 and 120 differentially expressed proteins (DEPs) after treatment with L3 and L3-K, respectively. L3 induced predominantly upregulated responses linked to metabolism, RNA processing, transport, and homeostasis, whereas L3-K mainly caused the downregulation of proteins involved in metabolism, transport, and cell structure. Both peptides disrupted ABC transporter-mediated nutrient uptake and elicited stress responses, while L3 specifically perturbed the mal regulon, indicative of broader transcriptional dysregulation. Complementary fluorescent dye displacement and in vitro transcription/translation assays demonstrated nonspecific DNA binding, stronger for L3 than L3-K, and potent inhibition of transcriptional and translational processes. Strikingly, inhibitory concentrations paralleled their minimum inhibitory concentrations, directly linking DNA binding and interference with central information processing to antimicrobial activity. These findings reveal that L3 and L3-K primarily act by targeting DNA and interfering with the transcription-translation machinery. Beyond offering mechanistic insights, this study underscores peptides' potential to act as scaffolds for next-generation antimicrobial peptides with DNA-binding and nonmembrane-lytic activity.", "doi": "10.1021/acsinfecdis.5c01000", "pmid": "41363146", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12797237"}], "notes": [], "created": "2026-01-27T13:32:34.240Z", "modified": "2026-01-27T13:32:34.344Z"}, {"entity": "publication", "iuid": "88fd0d987ac54f598427b2b468187b1e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88fd0d987ac54f598427b2b468187b1e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88fd0d987ac54f598427b2b468187b1e"}}, "title": "Quantitative optical nanoscopy of mitochondrial-derived vesicles in neurons classifies pre-peroxisomal and clearing organelles.", "authors": [{"family": "Coceano", "given": "Giovanna", "initials": "G", "orcid": "0000-0001-6579-0857", "researcher": {"href": "https://publications.scilifelab.se/researcher/e35c28e14e134fe3b4c9ab9efa129df0.json"}}, {"family": "Alvelid", "given": "Jonatan", "initials": "J", "orcid": "0000-0002-3554-9322", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf7f3ec8624f4cef96f96b3c28ffc6b8.json"}}, {"family": "Damenti", "given": "Martina", "initials": "M", "orcid": "0000-0002-4209-5381", "researcher": {"href": "https://publications.scilifelab.se/researcher/048f072498914ea9bc5fcc7d8ae0347e.json"}}, {"family": "Ferretti", "given": "Gabriella", "initials": "G", "orcid": "0000-0003-1848-5950", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc2029e30d4d4d6f9771f1e58d6fc929.json"}}, {"family": "Mueller", "given": "Johannes", "initials": "J"}, {"family": "Rorbach", "given": "Joanna", "initials": "J", "orcid": "0000-0002-2891-2840", "researcher": {"href": "https://publications.scilifelab.se/researcher/a069374613a7403b818ce7ca400f3627.json"}}, {"family": "Testa", "given": "Ilaria", "initials": "I", "orcid": "0000-0003-4005-4997", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d8e8420dada49d6a4ef1da7a06e02f1.json"}}], "type": "journal article", "published": "2026-01-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "pages": "419", "issn-l": "2041-1723"}, "abstract": "Healthy mitochondria are crucial for maintaining neuronal homeostasis. Their activity depends on a dynamic lipid and protein exchange through fusion, fission, and vesicular trafficking. Studying vesicles in neurons is challenging with conventional microscopy due to their small size, heterogeneity, and dynamics. We use multicolour stimulated emission depletion nanoscopy to uncover the ultrastructure of mitochondrial-derived vesicles (MDVs) in live neurons, biosensors to define their functional state, and a pulse-chase strategy to identify their turnover in situ. We identified three populations of vesicular structures: one transporting degradation products originating from oxidative stress, one shuttling cargo and newly translated proteins for local organelle biogenesis and one consisting of small, functional mitochondria. Furthermore, we provide evidence supporting that de novo peroxisomes biogenesis occurs via the fusion of endoplasmic reticulum and MDVs at mitochondrial sites. Our data provide mechanistic insight into organelle biogenesis driven by significant diversity in MDV morphology, functional state, and molecular composition.", "doi": "10.1038/s41467-025-68160-y", "pmid": "41507166", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12796351"}, {"db": "pii", "key": "10.1038/s41467-025-68160-y"}], "notes": [], "created": "2026-01-20T18:41:24.213Z", "modified": "2026-01-20T18:41:24.588Z"}, {"entity": "publication", "iuid": "2046ae6c4f484f9985d59ab7facdc2ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2046ae6c4f484f9985d59ab7facdc2ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2046ae6c4f484f9985d59ab7facdc2ba"}}, "title": "Tirzepatide reduces alcohol drinking and relapse-like behaviours in rodents.", "authors": [{"family": "Edvardsson", "given": "Christian E", "initials": "CE"}, {"family": "Adermark", "given": "Louise", "initials": "L"}, {"family": "Gottlieb", "given": "Sam", "initials": "S"}, {"family": "Alfreji", "given": "Safana", "initials": "S"}, {"family": "Emous", "given": "Thaynnam A", "initials": "TA"}, {"family": "Gouda", "given": "Yomna", "initials": "Y"}, {"family": "Thorsell", "given": "Annika", "initials": "A"}, {"family": "Vuji\u010di\u0107", "given": "Milica", "initials": "M"}, {"family": "Aran\u00e4s", "given": "Cajsa", "initials": "C"}, {"family": "Benrick", "given": "Anna", "initials": "A"}, {"family": "Wernstedt Asterholm", "given": "Ingrid", "initials": "I"}, {"family": "Lopez", "given": "Marcelo F", "initials": "MF"}, {"family": "Becker", "given": "Howard C", "initials": "HC"}, {"family": "Jerlhag", "given": "Elisabet", "initials": "E"}], "type": "journal article", "published": "2026-01-07", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "124", "pages": "106119", "issn-l": "2352-3964"}, "abstract": "Alcohol use disorder (AUD) remains a major public health problem, with few effective medications currently available. However, peptides of the gut-brain axis appear to offer promising therapeutic targets for AUD as they influence the mesolimbic reward circuitry.\n\nHere, we examined the effects of tirzepatide, a long-acting dual glucagon-like peptide-1 receptor (GLP-1R) and glucose-dependent insulinotropic polypeptide receptor (GIPR) agonist approved for diabetes and obesity, using behavioural assays (locomotor activity and conditioned place preference), alcohol intake paradigms (intermittent access two-bottle choice, drinking in the dark and the alcohol deprivation effect), and molecular analyses (microdialysis, electrophysiology and proteomics) in rodents.\n\nFirst, tirzepatide effectively attenuated the rewarding properties of alcohol, measured through locomotor stimulation, conditioned place preference, and accumbal dopamine release (P < 0.001). Subsequently, this GLP-1R/GIPR agonist dose-dependently reduced voluntary alcohol consumption (P < 0.001), prevented binge (P < 0.01) and relapse-like drinking (P < 0.001), and maintained efficacy during repeated administration (P < 0.001). Finally, tirzepatide induced sustained synaptic depression in the lateral septum (P < 0.05) and further altered histone regulatory proteins in this region (P < 0.05), suggesting a potential neural substrate for its effects. Moreover, the GLP-1R/GIPR agonist affected metabolic parameters including body weight (P < 0.001), adipose tissue mass (P < 0.01), hepatic triglycerides (P < 0.01) and circulating pro-inflammatory cytokines (P < 0.05).\n\nTogether, our findings suggest tirzepatide modulates alcohol-related behaviours through reward-related mechanisms while also affecting physiological consequences associated with long-term alcohol use. Given tirzepatide's established clinical use and the consistency of effects observed here, these results support further investigation for treating AUD and associated complications.\n\nThe study is supported by grants from the Swedish Research Council (2023-2600, 2020-00559, 2020-01463, 2024-03054), LUA/ALF (723941 & 1005347) from the Sahlgrenska University Hospital, Alcohol Research Council of the Swedish Alcohol Retailing Monopoly (FO2024-0048), National Institutes of Health (NIH) (P50 AA010761 & U01 AA014095), U.S. Department of Veterans Affairs Office of Research and Development (BLR&D I01BX000813 & IK6BX006299), Herbert & Karin Jacobssons Foundation (2024-Forskning-225), Adlerbertska Research Foundation (2024-791), Wilhelm & Martina Lundgren's Research Foundation (2024-SA-4698), \u00c5ke Wibergs Foundation (M24-0216), Swedish Diabetes Foundation (DIA 2024-898) and Mary von Sydow Foundation (2024-36 & 2024-185). Thaynnam A Emous held an international internship scholarship from the S\u00e3o Paulo Research Foundation (FAPESP), Process Number #2023/18470-5, while conducting research at the University of Gothenburg.", "doi": "10.1016/j.ebiom.2025.106119", "pmid": "41506148", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12808897"}, {"db": "pii", "key": "S2352-3964(25)00569-9"}], "notes": [], "created": "2026-01-27T13:33:58.738Z", "modified": "2026-01-27T13:33:58.753Z"}, {"entity": "publication", "iuid": "20af1880766c43ec92b67618ebf96e75", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20af1880766c43ec92b67618ebf96e75.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20af1880766c43ec92b67618ebf96e75"}}, "title": "Single-Cell Omics Analysis of Human Basophils Reveals Two Transcriptionally Distinct Populations.", "authors": [{"family": "Papavasileiou", "given": "Sofia", "initials": "S", "orcid": "0000-0002-4066-5715", "researcher": {"href": "https://publications.scilifelab.se/researcher/79bdcde693814787b551baca99852eb7.json"}}, {"family": "Mo", "given": "Jiezhen", "initials": "J"}, {"family": "Boey", "given": "Daryl", "initials": "D"}, {"family": "Wu", "given": "Chenyan", "initials": "C"}, {"family": "Tronstad", "given": "Magnus", "initials": "M"}, {"family": "Margerie", "given": "Lucille", "initials": "L", "orcid": "0000-0001-9537-1231", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5acd66266474d168d31cc60aa92294a.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Bachmann", "given": "J\u00f6rg A", "initials": "JA"}, {"family": "Low", "given": "Jing Hui", "initials": "JH"}, {"family": "Ong", "given": "Jocelyn", "initials": "J"}, {"family": "Blom", "given": "Lars Heede", "initials": "LH", "orcid": "0000-0003-2027-727X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a5bcf890d60428b9e6569c0d435c08d.json"}}, {"family": "Andiappan", "given": "Anand Kumar", "initials": "AK"}, {"family": "Nilsson", "given": "Gunnar", "initials": "G", "orcid": "0000-0001-6795-5512", "researcher": {"href": "https://publications.scilifelab.se/researcher/258ef97611dd4441a38e1baf2b517ecd.json"}}, {"family": "Dahlin", "given": "Joakim S", "initials": "JS", "orcid": "0000-0003-3007-9875", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d022071f86a451aba84b18fb0774461.json"}}], "type": "journal article", "published": "2026-01-07", "journal": {"title": "Allergy", "issn": "1398-9995", "issn-l": "0105-4538"}, "abstract": "Basophils are implicated in various diseases including allergies, but a comprehensive single-cell characterization of human basophils has yet to be performed. Here, we aimed to generate a single-cell omics-based reference resource of circulating human basophils, integrating transcriptomic and large-scale immunoprofiling data. We also sought to investigate basophil heterogeneity at the molecular level.\n\nCirculating basophils were analyzed using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq). Both short- and long-read single-cell RNA-sequencing platforms were used to capture the transcriptomic data.\n\nCITE-seq enabled accurate identification and profiling of side scatterlow lineage- CCR3+ Fc\u03b5RI+ basophils. Short-read single-cell RNA-sequencing data revealed two previously unresolved basophil populations, defined by 66 differentially expressed genes and reproducibly identified across donors. Despite the transcriptional differences, the populations displayed similar immunophenotypes based on more than 100 investigated cell surface markers. Long-read single-cell RNA-sequencing analysis confirmed the existence of the two populations and provided further insights into their gene expression profiles.\n\nWe present a multimodal single-cell resource that defines two novel transcriptionally distinct basophil populations. This resource, accessible through a user-friendly web interface, constitutes a cellular and molecular reference map for future studies of basophils in health and disease.", "doi": "10.1111/all.70209", "pmid": "41498390", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Single cell": "Collaborative", "NGI Short read": "Service", "NGI Long read": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-01-08T07:58:10.538Z", "modified": "2026-01-08T07:58:10.841Z"}, {"entity": "publication", "iuid": "9fc4953605de40198d0d1f18d4d4caf2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fc4953605de40198d0d1f18d4d4caf2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fc4953605de40198d0d1f18d4d4caf2"}}, "title": "Inflammatory protein profiles and shunt response in iNPH", "authors": [{"family": "Braun", "given": "Madelene", "initials": "M", "orcid": "0000-0001-8844-1756", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb656d2129504868a45c01ae52cdb700.json"}}, {"family": "Ekblom", "given": "Maria", "initials": "M"}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Nyholm", "given": "Dag", "initials": "D"}, {"family": "Kultima", "given": "Kim", "initials": "K", "orcid": "0000-0002-0680-1410", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ae376585168459681f5e2cae0c75b96.json"}}, {"family": "Virhammar", "given": "Johan", "initials": "J", "orcid": "0000-0001-9901-2949", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7c5d8e520cf483e9d4fbb1ce459aec5.json"}}], "type": "journal-article", "published": "2026-01-07", "journal": {"title": "Fluids Barriers CNS", "issn": "2045-8118", "volume": "23", "issue": "1", "pages": "5", "issn-l": null}, "abstract": "Neuroinflammation in the context of idiopathic normal pressure hydrocephalus (iNPH) is poorly studied. Currently, no single objective test can reliably predict outcomes after shunt surgery. The aim was to investigate whether neuroinflammatory proteins in cerebrospinal fluid (CSF) are associated with the characteristic symptoms of iNPH and whether they can predict outcome after shunting.\n\nNeuroinflammatory proteins were analyzed from preoperative CSF using proximity extension assay (PEA). In total, 92 proteins were analyzed from 74 patients with iNPH referred to shunt surgery at a single center, with follow-up at the same hospital. Symptoms were assessed before surgery and at follow-up (primarily 12 months post-surgery), graded with the Swedish iNPH scale. Associations between protein levels and preoperative symptoms, as well as outcome, were analyzed using linear regression models adjusted for age and sex; outcome models were additionally adjusted for baseline symptom level. Benjamini-Hochberg with a false discovery rate (FDR) of 5% was used to control for multiple analyses.\n\nOf the 92 analyzed proteins, 60 had detectable values greater than 50% and were included in the analyses. No associations between preoperative symptom severity and levels of inflammatory proteins remained statistically significant after correction for multiple comparisons (FDR 5%). After adjustment, CST5 showed a significant negative association with postoperative improvement in balance and continence domains (b = -34, q = 0.017 and b = -35, q = 0.026, respectively) but not for outcome in the total iNPH scale. A general trend was observed where higher levels of inflammatory proteins were linked to less favourable outcomes, although these did not remain statistically significant after correction.\n\nCST5 emerged as the only protein significantly associated with postoperative improvement after shunt surgery, suggesting a potential role in iNPH pathophysiology. Furthermore, no associations were observed between preoperative symptom severity and levels of inflammatory CSF proteins.\n\nThe online version contains supplementary material available at 10.1186/s12987-025-00751-9.", "doi": "10.1186/s12987-025-00751-9", "pmid": "41501840", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12784546"}, {"db": "pii", "key": "10.1186/s12987-025-00751-9"}], "notes": [], "created": "2026-02-10T10:00:00.564Z", "modified": "2026-03-24T09:15:02.947Z"}, {"entity": "publication", "iuid": "438c9e5e841c43789942d0c391dbba77", "links": {"self": {"href": "https://publications.scilifelab.se/publication/438c9e5e841c43789942d0c391dbba77.json"}, "display": {"href": "https://publications.scilifelab.se/publication/438c9e5e841c43789942d0c391dbba77"}}, "title": "TGF\u03b2 signaling mediates microglial resilience to spatiotemporally restricted myelin degeneration.", "authors": [{"family": "Zhu", "given": "Keying", "initials": "K", "orcid": "0000-0001-7500-1532", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b85d1ae8136464788be19d62a8863d7.json"}}, {"family": "Liu", "given": "Yun", "initials": "Y", "orcid": "0000-0001-5753-1265", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa51ce95224f46d8ac2a25652a0cded3.json"}}, {"family": "Min", "given": "Jin-Hong", "initials": "JH"}, {"family": "Joshua", "given": "Vijay", "initials": "V", "orcid": "0000-0002-2606-8180", "researcher": {"href": "https://publications.scilifelab.se/researcher/60cae01031724ad7b8d67851bc0d9b78.json"}}, {"family": "Lin", "given": "Jianing", "initials": "J"}, {"family": "Li", "given": "Yue", "initials": "Y", "orcid": "0000-0003-0584-1119", "researcher": {"href": "https://publications.scilifelab.se/researcher/12c8feb7f8914821905e56b6b81473ef.json"}}, {"family": "Kreutzmann", "given": "Judith C", "initials": "JC"}, {"family": "Guo", "given": "Yuxi", "initials": "Y"}, {"family": "Xia", "given": "Wenlong", "initials": "W"}, {"family": "Mohammadi", "given": "Elyas", "initials": "E"}, {"family": "Pieber", "given": "Melanie", "initials": "M"}, {"family": "Suerth", "given": "Valerie", "initials": "V"}, {"family": "Xia", "given": "Yiming", "initials": "Y"}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z"}, {"family": "Hugnot", "given": "Jean-Philippe", "initials": "JP"}, {"family": "Kanatani", "given": "Shigeaki", "initials": "S", "orcid": "0000-0003-2226-4288", "researcher": {"href": "https://publications.scilifelab.se/researcher/355335d5d964416883ccf63a312b69db.json"}}, {"family": "Uhl\u00e9n", "given": "Per", "initials": "P", "orcid": "0000-0003-1446-1062", "researcher": {"href": "https://publications.scilifelab.se/researcher/91c3e953634140b8974186ac0d7eac85.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Li", "given": "Xiaofei", "initials": "X", "orcid": "0000-0002-9991-7534", "researcher": {"href": "https://publications.scilifelab.se/researcher/d90bb6581d134277924377269eef88b9.json"}}, {"family": "Fancy", "given": "Stephen P J", "initials": "SPJ", "orcid": "0000-0002-2818-8258", "researcher": {"href": "https://publications.scilifelab.se/researcher/0afaa662c4d943579e4823dba3dae348.json"}}, {"family": "Sarlus", "given": "Heela", "initials": "H", "orcid": "0000-0001-7880-9828", "researcher": {"href": "https://publications.scilifelab.se/researcher/9985f00d25dc4440b4e9a10ec5c3a69f.json"}}, {"family": "Harris", "given": "Robert A", "initials": "RA", "orcid": "0000-0003-4990-509X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b0733d3c25145139f42cad897d6726b.json"}}, {"family": "Lund", "given": "Harald", "initials": "H", "orcid": "0000-0001-8046-0805", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fe4902c355449e4812008d4ad7a37e0.json"}}], "type": "journal article", "published": "2026-01-02", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256"}, "abstract": "Microglia survey and regulate central nervous system myelination during embryonic development and adult homeostasis. However, whether microglia-myelin interactions are spatiotemporally regulated remains unexplored. Here, by examining spinal cord white matter tracts in mice, we determined that myelin degeneration was particularly prominent in the dorsal column (DC) during normal aging. This was accompanied by molecular and functional changes in DC microglia as well as an upregulation of transforming growth factor beta (TGF)\u03b2 signaling. Disrupting TGF\u03b2 signaling in microglia led to unrestrained microglial responses and myelin loss in the DC, accompanied by neurological deficits exacerbated with aging. Single-nucleus RNA-sequencing analyses revealed the emergence of a TGF\u03b2 signaling-sensitive microglial subset and a disease-associated oligodendrocyte subset, both of which were spatially restricted to the DC. We further discovered that microglia rely on a TGF\u03b2 autocrine mechanism to prevent damage of myelin in the DC. These findings demonstrate that TGF\u03b2 signaling is crucial for maintaining microglial resilience to myelin degeneration in the DC during aging. This highlights a previously unresolved checkpoint mechanism of TGF\u03b2 signaling with regional specificity and spatially restricted microglia-oligodendrocyte interactions.", "doi": "10.1038/s41593-025-02161-4", "pmid": "41482590", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-025-02161-4"}], "notes": [], "created": "2026-01-07T10:54:23.366Z", "modified": "2026-01-07T10:54:23.929Z"}, {"entity": "publication", "iuid": "053ef45f515a4c6d94ba0ee3a1b5a74a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/053ef45f515a4c6d94ba0ee3a1b5a74a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/053ef45f515a4c6d94ba0ee3a1b5a74a"}}, "title": "Genome Shows no Recent Inbreeding in Near-Extinction Woolly Rhinoceros Sample Found in Ancient Wolf's Stomach.", "authors": [{"family": "Gu\u00f0j\u00f3nsd\u00f3ttir", "given": "S\u00f3lveig M", "initials": "SM", "orcid": "0009-0002-6435-4409", "researcher": {"href": "https://publications.scilifelab.se/researcher/67d580e28f1f4e9ea90b46b330b6dcff.json"}}, {"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7355501dddb4508bf453c7c1ad9f107.json"}}, {"family": "Leme\u017e", "given": "\u0160pela", "initials": "\u0160", "orcid": "0000-0002-0387-1421", "researcher": {"href": "https://publications.scilifelab.se/researcher/381dee4d331a43369d747adc51275fea.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Stanton", "given": "David W G", "initials": "DWG", "orcid": "0000-0002-9753-3166", "researcher": {"href": "https://publications.scilifelab.se/researcher/2732b89a34b54967bcb87811cdc3fb1c.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Fedorov", "given": "Sergey", "initials": "S", "orcid": "0000-0001-8179-740X", "researcher": {"href": "https://publications.scilifelab.se/researcher/856215bb926b471c9d74e7408715f8e6.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}], "type": "journal article", "published": "2026-01-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "18", "issue": "1", "issn-l": "1759-6653"}, "abstract": "Using temporarily spaced high-coverage ancient genomes, we can assess population decline prior to extinction. However, finding suitable ancient remains for recovering this type of data is challenging. Here, we sequenced a high-coverage genome from muscle tissue of a 14,400-year-old woolly rhinoceros (Coelodonta antiquitatis)-a cold-adapted herbivore that went extinct \u223c14,000-years ago-found inside a permafrost-preserved wolf's stomach. We compared genome-wide diversity, inbreeding, genetic load, and population size changes in this sample with two other Late Pleistocene Siberian woolly rhinoceros. We found no evidence of population size decline, nor any genomic erosion, shortly prior to the species' demise. Given the few long homozygous segments, typically indicative of recent inbreeding, we infer a stable population size only a few centuries before extinction. Thus, the woolly rhinoceros' extinction likely happened rapidly, during the B\u00f8lling-Aller\u00f8d interstadial. This study demonstrates the ability to recover high-quality DNA from unlikely sources to elucidate species' extinction dynamics.", "doi": "10.1093/gbe/evaf239", "pmid": "41530912", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12799484"}, {"db": "pii", "key": "8414728"}], "notes": [], "created": "2026-01-22T13:27:26.594Z", "modified": "2026-01-22T13:27:27.263Z"}, {"entity": "publication", "iuid": "cc47692d5ce54490b075f561042eafa5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc47692d5ce54490b075f561042eafa5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc47692d5ce54490b075f561042eafa5"}}, "title": "Acute high-dose irradiation disrupts cell adhesion and Silk-Ovarioid formation in human primary ovarian cells", "authors": [{"family": "Deligiannis", "given": "Spyridon Panagiotis", "initials": "SP"}, {"family": "Li", "given": "Tianyi", "initials": "T"}, {"family": "Moussaud-Lamodi\u00e8re", "given": "Elisabeth", "initials": "E", "orcid": "0000-0002-2359-6519", "researcher": {"href": "https://publications.scilifelab.se/researcher/70a0f932253042239c1d38ea00ca0018.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "Akos", "initials": "A", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Damdimopoulos", "given": "Anastasios", "initials": "A"}, {"family": "Lavogina", "given": "Darja", "initials": "D"}, {"family": "Papaikonomou", "given": "Kiriaki", "initials": "K"}, {"family": "Zubarev", "given": "Roman", "initials": "R", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}, {"family": "Acharya", "given": "Ganesh", "initials": "G"}, {"family": "Velthut-Meikas", "given": "Agne", "initials": "A", "orcid": "0000-0003-1927-9016", "researcher": {"href": "https://publications.scilifelab.se/researcher/3371af7256714f478d42af5cf868134d.json"}}, {"family": "Damdimopoulou", "given": "Pauliina", "initials": "P", "orcid": "0000-0001-8458-0855", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d258c0f0d9b417ea4608769fc3ebaaf.json"}}, {"family": "Salumets", "given": "Andres", "initials": "A", "orcid": "0000-0002-1251-8160", "researcher": {"href": "https://publications.scilifelab.se/researcher/88dcf4bacf5c4792bbfd111495d43595.json"}}, {"family": "Di Nisio", "given": "Valentina", "initials": "V", "orcid": "0000-0002-8435-7925", "researcher": {"href": "https://publications.scilifelab.se/researcher/bee1509ba58840f597b7fccc778a0a20.json"}}], "type": "journal-article", "published": "2026-01-02", "journal": {"title": "J Ovarian Res", "issn": "1757-2215", "issn-l": null, "volume": "19", "issue": "1", "pages": null}, "abstract": "Radiotherapy is a cornerstone of cancer treatment; however, its effects on healthy ovarian somatic cells remain largely unexplored. This study addresses this gap by investigating how human cortical and medullary primary ovarian cells (cPOCs and mPOCs, respectively) respond to acute, high-dose X-ray exposure in vitro.\n\nOvarian tissue was obtained from eight patients (aged 23\u201336 years) undergoing gender-affirming surgery at Karolinska University Hospital in Huddinge, Sweden. The tissue was separated into cortex and medulla and dissociated into cPOCs and mPOCs. Monolayer cultures of cPOCs and mPOCs were exposed to 10 Gy X-rays upon reaching confluency, or left unexposed as paired controls. Following irradiation, cells were assessed for ATP content and mitochondrial dehydrogenase activity, followed by immunofluorescence staining, bulk RNA sequencing (Illumina Stranded mRNA Prep Ligation protocol; sequencing on the Illumina NovaSeq 6000 platform), bulk proteomic analysis (liquid chromatography\u2013tandem mass spectrometry), and a functional assay for assessing their ability to form 3D Silk-Ovarioids.\n\nWhile irradiation did not significantly affect cell viability, immunofluorescence analyses revealed alterations in DNA damage response, apoptosis, and cell cycle regulation. Transcriptomic analysis showed minimal changes at 1 h post-irradiation in both cPOCs and mPOCs. However, marked shifts in transcriptomic profiles were observed at 4 h (2,810 and 2,540 DEGs in cPOCs and mPOCs, respectively) and at 24 h (2,462 and 2,802 DEGs, respectively), including upregulation of the p53 pathway and downregulation of MYC targets, E2F targets, the G2/M checkpoint, and the mTORC1 pathway. At the proteomic level, differentially expressed proteins associated with cell adhesion, focal adhesion, and cadherin binding were detected at 24 h post-irradiation. Functionally, irradiated cells demonstrated an impaired capacity to self-organize into 3D Silk-Ovarioids, indicating compromised cell\u2013cell adhesion.\n\nThese findings reveal a novel mechanism by which radiotherapy may damage ovarian tissue independently of follicular loss, underscoring the need for targeted strategies to preserve somatic cell function in fertility preservation protocols.\n\nThe online version contains supplementary material available at 10.1186/s13048-025-01932-8.", "doi": "10.1186/s13048-025-01932-8", "pmid": "41485059", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": null}, "xrefs": [{"db": "pmc", "key": "PMC12930946"}, {"db": "pii", "key": "10.1186/s13048-025-01932-8"}], "notes": [], "created": "2026-01-07T10:51:06.159Z", "modified": "2026-03-24T09:15:33.835Z"}, {"entity": "publication", "iuid": "f48f131387f44524b2e0db88864b0c45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f48f131387f44524b2e0db88864b0c45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f48f131387f44524b2e0db88864b0c45"}}, "title": "Using Historic and Contemporary Genomes to Assess the Genetic Consequences of a Population Decline in an Endangered Tern Population.", "authors": [{"family": "Schnelle", "given": "Anna", "initials": "A", "orcid": "0000-0002-5403-8421", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7a663ebd957425293ede7c37c1a2a34.json"}}, {"family": "Rollins", "given": "Robert E", "initials": "RE", "orcid": "0000-0002-5779-7001", "researcher": {"href": "https://publications.scilifelab.se/researcher/ceba437696254c37b039fa4631200a74.json"}}, {"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Cecere", "given": "Jacopo G", "initials": "JG"}, {"family": "Serra", "given": "Lorenzo", "initials": "L", "orcid": "0000-0002-8911-8050", "researcher": {"href": "https://publications.scilifelab.se/researcher/de52abed5b814b7c82d985c448cafa7e.json"}}, {"family": "Guti\u00e9rrez", "given": "Jorge S", "initials": "JS"}, {"family": "Masero", "given": "Jose A", "initials": "JA"}, {"family": "Risch", "given": "Markus", "initials": "M"}, {"family": "Bouwhuis", "given": "Sandra", "initials": "S", "orcid": "0000-0003-4023-1578", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f1fb8d7e1e4b0a94aac306ba67006a.json"}}, {"family": "Liedvogel", "given": "Miriam", "initials": "M"}], "type": "journal article", "published": "2026-01-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "19", "issue": "1", "pages": "e70192", "issn-l": "1752-4571"}, "abstract": "Many migratory species have experienced severe population declines, but the genetic consequences of such declines are still rarely assessed. The last Central European population of gull-billed terns (Gelochelidon nilotica) has declined from 500 breeding pairs in the 1940s to 52 in 2025, whereas Mediterranean populations of this migratory waterbird still thrive. Here, we compare whole-genome sequencing (WGS) data among the declining population, two thriving populations and the ancestors of the declining population. We find comparable nucleotide diversity, but lower observed heterozygosity in the Central European population compared to the Mediterranean populations. The contemporary samples show some population structure as well, although admixture analyses and low genetic differentiation (F ST) still suggest potential population connectivity. Museum specimens from the historic population reveal an increased level of genetic diversity compared to the contemporary population, with effective population size estimates suggesting two past population declines. While inbreeding coefficients (F ROH) in the current Central European population are significantly higher than in the historic population, they are similar to those in the Mediterranean populations. These results suggest that population structure may be emerging, and that although inbreeding is not yet at worrisome levels in the last Central European population of gull-billed terns, it may be on the rise. If this endangered population remains small and isolation manifests, the effects of inbreeding depression may become more pronounced over time, potentially reducing fitness and increasing the risk of extinction.", "doi": "10.1111/eva.70192", "pmid": "41488439", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12759046"}, {"db": "pii", "key": "EVA70192"}], "notes": [], "created": "2026-01-07T10:52:49.278Z", "modified": "2026-01-07T10:52:49.806Z"}, {"entity": "publication", "iuid": "9e497d987d264f8bade35c9d92a568de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e497d987d264f8bade35c9d92a568de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e497d987d264f8bade35c9d92a568de"}}, "title": "Long-term heating differently impacts diversity and seasonal dynamics of prokaryotes and micro-eukaryotes in Baltic Sea coastal biofilm communities.", "authors": [{"family": "Svendsen", "given": "Ida Krogsgaard", "initials": "IK", "orcid": "0000-0003-3265-6234", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d420e1d66fa445e89f9cc0fc4432a3a.json"}}, {"family": "Rula", "given": "Iryna", "initials": "I", "orcid": "0000-0003-0906-0301", "researcher": {"href": "https://publications.scilifelab.se/researcher/e235bf754668420cb161059fe6d49dc0.json"}}, {"family": "Nilsson", "given": "Emelie", "initials": "E", "orcid": "0000-0001-5103-214X", "researcher": {"href": "https://publications.scilifelab.se/researcher/996d4cbfd1f84e5b9f5847e47223c22d.json"}}, {"family": "Sunde", "given": "Johanna", "initials": "J", "orcid": "0000-0002-3145-1475", "researcher": {"href": "https://publications.scilifelab.se/researcher/972ff747b7044a6096583673286e9443.json"}}, {"family": "Li", "given": "Songjun", "initials": "S", "orcid": "0009-0008-4816-2451", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa0c5a7e34da45c2aca6f8de83af14b5.json"}}, {"family": "Hylander", "given": "Samuel", "initials": "S", "orcid": "0000-0002-3740-5998", "researcher": {"href": "https://publications.scilifelab.se/researcher/47f71565ec50426e9d4893a5335e5fa3.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}, {"family": "Forsman", "given": "Anders", "initials": "A", "orcid": "0000-0001-9598-7618", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a605b671cd3414d9c75c2408b74d3de.json"}}, {"family": "Salis", "given": "Romana Katerina", "initials": "RK", "orcid": "0000-0001-7724-4984", "researcher": {"href": "https://publications.scilifelab.se/researcher/04732c60ef2040289f7a5664aa697a7d.json"}}], "type": "journal article", "published": "2026-01-00", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "6", "issue": "1", "pages": "ycag101", "issn-l": null}, "abstract": "Warming temperatures, heat waves, and altered conditions associated with climate change affect biodiversity and ecological processes across environments, with coastal zones being particularly vulnerable. Biofilm-forming organisms in shallow coastal areas are taxonomically diverse and include bacteria, fungi, and algae that contribute to energy and nutrient cycling along with providing habitats and food for species at the base of the food web. To understand how biofilm-forming organisms respond differently to spatiotemporally changing environmental conditions, seasonal sampling was performed in a Baltic Sea bay that has undergone 50 years of thermal heating, an unaffected nearby control bay, and a temperature gradient along an exposed coastline between the bays. The diversity, composition, and seasonal dynamics of the biofilm communities differed between the three environments largely due to temperature and water chemistry, with biofilms in the heated bay being more similar across seasons compared with the control bay and the gradient, and with prokaryotes exhibiting stronger spatial heterogeneity and seasonal dynamics compared to micro-eukaryotes. In the gradient, the dominating taxonomic groups were distinct, community composition was primarily influenced by seasonal turnover and wave exposure, and alpha diversity of prokaryotes decreased with increasing temperature. Seasonal shifts in the composition of micro-eukaryotic heterotrophs, phototrophs, and mixotrophs differed between environments, with heterotrophs being more dominant at higher temperatures. In conclusion, these contrasting responses indicated that climate warming may disproportionately impact different components of coastal biofilm communities, potentially decoupling key ecological processes and reducing community resilience in Baltic Sea coastal habitats.", "doi": "10.1093/ismeco/ycag101", "pmid": "42147142", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13174331"}, {"db": "pii", "key": "ycag101"}], "notes": [], "created": "2026-06-08T17:26:27.957Z", "modified": "2026-06-08T17:26:28.388Z"}, {"entity": "publication", "iuid": "62aeb5e95c7f40e5b971a1dd1f521f6e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62aeb5e95c7f40e5b971a1dd1f521f6e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62aeb5e95c7f40e5b971a1dd1f521f6e"}}, "title": "Genetic risk factors and clinical manifestations of systemic lupus erythematosus: Large-scale analysis of genetic predisposition and disease subtypes.", "authors": [{"family": "Reid", "given": "Sarah", "initials": "S"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK", "orcid": "0000-0003-1382-2321", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c7bae5a05ac47eeac96547ca7336767.json"}}, {"family": "Pucholt", "given": "Pascal", "initials": "P"}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Frodlund", "given": "Martina", "initials": "M"}, {"family": "Lerang", "given": "Karoline", "initials": "K"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC"}, {"family": "Molberg", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Rudin", "given": "Anna", "initials": "A", "orcid": "0000-0002-4137-1276", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa2b87964bc0472b88fa4267ee23c483.json"}}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}, {"family": "Leonard", "given": "Dag", "initials": "D", "orcid": "0000-0002-6275-7282", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ed25c2f495484db4757f4fef51abae.json"}}], "type": "journal article", "published": "2026-01-00", "journal": {"title": "J. Intern. Med.", "issn": "1365-2796", "volume": "299", "issue": "1", "pages": "95-108", "issn-l": "0954-6820"}, "abstract": "Systemic lupus erythematosus (SLE) is an autoimmune disease with a heterogenous clinical picture. This study aimed to link genetic SLE predisposition with relevant clinical manifestations.\n\nDatasets best corresponding to the 11 American College of Rheumatology 1982 (ACR-82) classification criteria for SLE in a large, public database (FinnGen consortium, >218,000 individuals) were identified. Mendelian randomization analysis was conducted to evaluate the effect of a high genetic SLE predisposition on each manifestation. Next, validation was conducted in a clinical SLE cohort comprising 1487 genotyped Scandinavian patients with detailed clinical data. Based on the public datasets, genetic risk scores (GRSs) for each relevant manifestation were constructed for each patient. Associations between each GRS and the corresponding ACR-82 criterion were evaluated using logistic regression.\n\nIn the FinnGen biobank, the cumulative effect of the 57 SLE risk SNPs was associated with an increased risk of rosacea, OR 1.09 (1.03-1.16), polyarthropathies, OR 1.10 (1.06-1.14), pleural effusions, OR 1.09 (1.04-1.14), and hemolytic anemia, OR 1.32 (1.10-1.58). In the clinical cohort, 5 of the 11 GRSs generated from the public datasets were associated with their corresponding ACR-82 criterion: arthritis, OR 1.15 (1.02-1.31), renal disorder, OR 1.15 (1.04-1.29), neurologic disorder, OR 1.24 (1.04-1.47), hematologic disorder, OR 1.12 (1.00-1.24), and immunologic disorder, OR 1.37 (1.22-1.56).\n\nThe findings demonstrate that known SLE risk gene variants play a role in the development of at least half of the ACR-82 criteria for SLE, indicating a future possibility of using genetics to predict a variety of disease sub-phenotypes in SLE.", "doi": "10.1111/joim.70040", "pmid": "41200769", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12678220"}], "notes": [], "created": "2026-06-01T08:45:42.226Z", "modified": "2026-06-01T08:45:42.343Z"}, {"entity": "publication", "iuid": "acea30367c0e4b8596dda08be1a22c72", "links": {"self": {"href": "https://publications.scilifelab.se/publication/acea30367c0e4b8596dda08be1a22c72.json"}, "display": {"href": "https://publications.scilifelab.se/publication/acea30367c0e4b8596dda08be1a22c72"}}, "title": "Exploring the Substitution of the C21-OAc Moiety in [11]Cytochalasans: Synthesis and Evaluation of Fluorophore Conjugates.", "authors": [{"family": "Kagho", "given": "Mervic D", "initials": "MD", "orcid": "0000-0003-3714-7738", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0d7812a50e942f09ec2df8bb7d6e287.json"}}, {"family": "Schmidt", "given": "Katharina", "initials": "K", "orcid": "0000-0003-1512-1748", "researcher": {"href": "https://publications.scilifelab.se/researcher/9127b79482d64c53acf2b175e32079f9.json"}}, {"family": "Chakrabarti", "given": "Aishi", "initials": "A", "orcid": "0009-0002-9704-0801", "researcher": {"href": "https://publications.scilifelab.se/researcher/74cbfb341f864b898bade9ee188639fe.json"}}, {"family": "Karger", "given": "Marius", "initials": "M", "orcid": "0009-0003-4513-3923", "researcher": {"href": "https://publications.scilifelab.se/researcher/78022aba123d4ba1b96070b360b1da01.json"}}, {"family": "Lambert", "given": "Christopher", "initials": "C", "orcid": "0000-0002-1899-8214", "researcher": {"href": "https://publications.scilifelab.se/researcher/89ab525eba11464c9e453b43c71d6678.json"}}, {"family": "Hauser", "given": "Maurice", "initials": "M", "orcid": "0009-0003-0758-8521", "researcher": {"href": "https://publications.scilifelab.se/researcher/1561beed9521484fb1e864873db8ac8c.json"}}, {"family": "Cox", "given": "Russell J", "initials": "RJ", "orcid": "0000-0002-1844-0157", "researcher": {"href": "https://publications.scilifelab.se/researcher/f285a288c52b44789d145e82b884eb40.json"}}, {"family": "Rottner", "given": "Klemens", "initials": "K", "orcid": "0000-0003-4244-4198", "researcher": {"href": "https://publications.scilifelab.se/researcher/272d787b62ee4e6b80920ec6d1a8e456.json"}}, {"family": "Stadler", "given": "Marc", "initials": "M", "orcid": "0000-0002-7284-8671", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd617bba3c524e3092538ea086715b62.json"}}, {"family": "Stradal", "given": "Theresia E", "initials": "TE", "orcid": "0000-0002-0352-9474", "researcher": {"href": "https://publications.scilifelab.se/researcher/7981da95069947799a3deccfad2de025.json"}}, {"family": "Klahn", "given": "Philipp", "initials": "P", "orcid": "0000-0003-4713-2345", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c6f067dc85a4e12b3593401e34e36d6.json"}}], "type": "journal article", "published": "2026-01-00", "journal": {"title": "ChemBioChem", "issn": "1439-7633", "volume": "27", "issue": "1", "pages": "e202500794", "issn-l": "1439-4227"}, "abstract": "The actin cytoskeleton plays a central role in cellular organization and dynamics, yet the tools available for targeting actin function remain limited. Cytochalasans represent a large class of actin-targeting natural products that are readily cell permeable with varying cytotoxicity and actin-targeting capabilities in mammalian cells. Their pharmacologic exploitation not only requires an understanding of their mode of action but also exact knowledge of how they can be derivatized without affecting their bioactivity. Herein, the design, synthesis, and evaluation of five fluorescently labeled [11]cytochalasan derivatives generated from pyrichalasin H (PyriH) and 19,20-epoxycytochalasin C (EpoxyCytoC) are reported. Guided by molecular docking, the C21-OAc moiety is identified as a promising site for tag attachment without disrupting actin binding. Semisynthetic modifications enable the conjugation of different dyes to PyriH and EpoxyCytoC scaffolds. Moreover, the effect of linkers separating cytochalasans and dyes is analyzed. Biological evaluation supplemented by in vitro assays to additionally interrogates their activities on the assembly of pure actin filaments revealing distinct activity profiles. Together, this study compares permeability, cytotoxicity, and actin binding of five novel [11]cytochalasan probes bearing substitutions of the C21-OAc moiety. These findings establish the C21-OAc position as a versatile functionalization site and provide a framework for developing next generation cytochalasan-based actin-targeting probes.", "doi": "10.1002/cbic.202500794", "pmid": "41306084", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12781145"}], "notes": [], "created": "2026-01-27T13:35:40.349Z", "modified": "2026-01-27T13:35:41.265Z"}, {"entity": "publication", "iuid": "33c0bbe9b62046fe9c45cf73bd92f4cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33c0bbe9b62046fe9c45cf73bd92f4cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33c0bbe9b62046fe9c45cf73bd92f4cc"}}, "title": "Dynamic interaction of the Yersinia pseudotuberculosis type three secretion system proteins LcrV and LcrG.", "authors": [{"family": "Mangu", "given": "Jagadish Chandra Kumar", "initials": "JCK", "orcid": "0000-0003-1850-1412", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a3713eb7af24389a3f32c1e5d8dd7c9.json"}}, {"family": "Rogne", "given": "Per", "initials": "P", "orcid": "0000-0002-3687-9200", "researcher": {"href": "https://publications.scilifelab.se/researcher/31042ecc88a94cd6b97cef0508da93fd.json"}}, {"family": "Mattsson", "given": "Jonna", "initials": "J", "orcid": "0000-0002-5294-7808", "researcher": {"href": "https://publications.scilifelab.se/researcher/894626ea67fd459eb08e4a9c4768fb09.json"}}, {"family": "Hultgren", "given": "Lucas", "initials": "L"}, {"family": "Gahlot", "given": "Kumar D", "initials": "KD"}, {"family": "Lamy", "given": "Ana\u00efs", "initials": "A", "orcid": "0000-0001-9757-100X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3886e3714e8142778455c4b96e1a2983.json"}}, {"family": "Berntsson", "given": "Ronnie P-A", "initials": "RP"}, {"family": "Johansson", "given": "Lennart B-\u00c5", "initials": "LB"}, {"family": "Francis", "given": "Matthew S", "initials": "MS"}, {"family": "Wolf-Watz", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2026-01-00", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": "35", "issue": "1", "pages": "e70400", "issn-l": "0961-8368"}, "abstract": "Yersinia pathogenicity is dependent on polarized translocation of effector proteins via the type III secretion system (T3SS). The tip complex situated on the needle structure of the T3SS is required for contact with the eukaryotic host membrane and is to an extent composed of pentameric LcrV. LcrV is a multifunctional protein that also acts as a regulator of the T3SS by virtue of forming a high-affinity complex in the cytoplasm with its chaperone, LcrG. By employing a structure-based approach centered on mass spectrometry, FRET and NMR spectroscopy, we demonstrated that the LcrV-LcrG complex is best described as a multivalent complex, and that the N-terminal domain of LcrV contributes by negatively affecting the LcrG binding affinity. The N-terminal domain of LcrV is dynamic and undergoes a conformational change to accommodate LcrG binding. 19F NMR spectroscopy analysis suggests that the conformational change is an intrinsic property of the protein, which agrees with a conformational selection model. An analysis of effector secretion into a culture supernatant demonstrated that the low synthesis and low secretion phenotypes of a LcrV mutant where the N-terminal domain has been removed are linked to the structure, interactions and stability of the LcrV N-terminal domain. In summary, our results add insights into the dynamics of LcrV and its complex with LcrG.", "doi": "10.1002/pro.70400", "pmid": "41427733", "labels": {"Swedish NMR Centre": "Service", "Structural Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12720783"}], "notes": [], "created": "2026-02-20T13:00:10.096Z", "modified": "2026-04-24T09:00:04.729Z"}, {"entity": "publication", "iuid": "f8ff8e625f5d45218a355407b7607936", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8ff8e625f5d45218a355407b7607936.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8ff8e625f5d45218a355407b7607936"}}, "title": "Co-exposure to PFAS and hydroxylated PCBs is associated with increased odds of multiple sclerosis", "authors": [{"family": "Vaivade", "given": "Aina", "initials": "A"}, {"family": "Sreenivasan", "given": "Akshai Parakkal", "initials": "AP", "orcid": "0000-0002-7293-6487", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b2f62a3bda9471d9227a6924b8adf7c.json"}}, {"family": "Erngren", "given": "Ida", "initials": "I", "orcid": "0000-0001-7867-9525", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8a16aaaf5194acba6b8649690a101d8.json"}}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Emami Khoonsari", "given": "Payam", "initials": "P"}, {"family": "Siljebo", "given": "Jakob", "initials": "J"}, {"family": "Al-Grety", "given": "Asma", "initials": "A"}, {"family": "Carlsson", "given": "Henrik", "initials": "H", "orcid": "0000-0001-5558-6641", "researcher": {"href": "https://publications.scilifelab.se/researcher/de9581804a0b4b22991b34ebe89e9017.json"}}, {"family": "\u00c5kerfeldt", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "Hedstr\u00f6m", "given": "Anna Karin", "initials": "AK", "orcid": "0000-0002-6612-4749", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4a1c4b315cd4a09b8f98a87b6cd2fba.json"}}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Alfredsson", "given": "Lars", "initials": "L", "orcid": "0000-0003-1688-6697", "researcher": {"href": "https://publications.scilifelab.se/researcher/6df230614a8a448e8607e03480169658.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Burman", "given": "Joachim", "initials": "J", "orcid": "0000-0002-7045-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b9b82661abc49baaeac34bfcfc45321.json"}}, {"family": "Kultima", "given": "Kim", "initials": "K", "orcid": "0000-0002-0680-1410", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ae376585168459681f5e2cae0c75b96.json"}}], "type": "journal-article", "published": "2026-01-00", "journal": {"title": "Environment International", "issn": "0160-4120", "issn-l": "0160-4120", "volume": "207", "issue": null, "pages": "109993"}, "abstract": "Persistent organic pollutants often co-occur in human exposure environments, yet their combined effects on disease risk remain poorly understood. This study examined associations between serum concentrations of 14 per- and polyfluorinated substances (PFAS) and three hydroxylated polychlorinated biphenyls (OH-PCBs) and the onset of multiple sclerosis (MS), utilizing data from the Swedish population-based Epidemiological Investigation of Multiple Sclerosis (EIMS) cohort, comprising 907 MS cases and 907 matched controls. We employed single-substance logistic regression and quantile g-computation to evaluate cumulative and individual compound associations. We considered linear and non-linear risk patterns while adjusting for lifestyle factors and MS-associated HLA alleles. Our analysis revealed non-linear associations for several individual compounds, particularly perfluorooctane sulfonic acid (PFOS), perfluorononanoic acid, 2,2',3,4',5,5',6-heptachloro-4-biphenylol (4-OH-CB187), and 2,2',4,4',5,5'-, Hexachloro-3-biphenylol (3-OH-CB153), with increased odds of MS. Interaction analyses further indicated that the association between PFOS and MS odds was modified by the presence of the HLA-B*44:02 allele, known for its protective effect on MS risk. Mixture modeling highlighted that combined exposures to PFAS and OH-PCBs significantly increased MS odds, even when associations for individual compounds were weak or absent. These findings emphasize the complexity of associations between environmental contaminants, lifestyle and genetic risk factors, and the odds of MS. They underscore the importance of addressing co-exposure in environmental health research and call for further studies to elucidate underlying biological mechanisms.", "doi": "10.1016/j.envint.2025.109993", "pmid": "41411973", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0160-4120(25)00744-5"}], "notes": [], "created": "2026-02-10T09:53:14.232Z", "modified": "2026-03-24T09:16:23.730Z"}, {"entity": "publication", "iuid": "936c13b506f14b1f90ff1ab6d0359b4f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/936c13b506f14b1f90ff1ab6d0359b4f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/936c13b506f14b1f90ff1ab6d0359b4f"}}, "title": "Benchmarking of single nuclei RNA-seq methods on human post-mortem brain tissue", "authors": [{"family": "Nikouei", "given": "Kasra", "initials": "K"}, {"family": "Gruyters", "given": "Elin", "initials": "E"}, {"family": "Memic", "given": "Fatima", "initials": "F", "orcid": "0000-0002-8876-1212", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea5dcdcbf16f4caab9cea24133389afb.json"}}, {"family": "Stockmeier", "given": "Craig A", "initials": "CA", "orcid": "0000-0003-1861-1013", "researcher": {"href": "https://publications.scilifelab.se/researcher/89ebb5b73b9a42498192d35aea2d92c5.json"}}, {"family": "Hjerling-Leffler", "given": "Jens", "initials": "J", "orcid": "0000-0002-4539-1776", "researcher": {"href": "https://publications.scilifelab.se/researcher/51675f0ff9aa47d89d6b2eb84a14820a.json"}}], "type": "journal-article", "published": "2026-01-00", "journal": {"title": "Genomics", "issn": "0888-7543", "issn-l": null, "volume": "118", "issue": "1", "pages": "111184"}, "abstract": "Molecular analysis of human post-mortem brain tissue holds the promise to identify disease associated mechanisms. Single nuclei RNA-sequencing (snRNA-seq) is a powerful tool for molecular-level investigations of human brain tissue with cell type resolution. In the fast-developing field of post-mortem snRNA-seq, the samples sizes of case/control studies have drastically increased over the last years. Still, to overcome genetic variability across individuals and to investigate the many relevant brain regions that have not yet been sampled, even larger cohorts are necessary. It is thus important to benchmark snRNA-seq methods against each other on relevant tissue. We compared five such methods, 10\u00d7 Genomics v3.1, 10\u00d7 Genomics Flex Gene Expression, Parse Biosciences Evercode v2, PIPseq v5.0 from Fluent Biosciences (now acquired by Illumina) and Smart-seq3xpress, using fresh frozen post-mortem human forebrain tissue samples. Using tissue samples from the same three donors for all methods, our investigation revealed comparable overall technical performance among the five methods but suggests that biological variability was better captured with Smart-seq3xpress. We could not model the effect of sample quality, which limits the generalizability of our results. Thus, our study suggests that the selection of snRNA-seq method should mainly be informed by the need of specific data and practical experimental considerations such as hardware requirements, ability to multiplex, tissue quantity input requirements, and transportation of samples/tissues.", "doi": "10.1016/j.ygeno.2025.111184", "pmid": "41453581", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": null}, "xrefs": [{"db": "pii", "key": "S0888-7543(25)00200-9"}], "notes": [], "created": "2026-01-13T10:27:04.485Z", "modified": "2026-03-24T09:16:35.858Z"}]}