{"entity": "researcher", "timestamp": "2026-08-20T21:01:26.757Z", "family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "affiliations": ["Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/8638ca04ea7f4ff8a191f3c6969b1394.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/8638ca04ea7f4ff8a191f3c6969b1394"}}, "publications": [{"entity": "publication", "iuid": "2c33ff0022514cc0a34221286892e5bb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2c33ff0022514cc0a34221286892e5bb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2c33ff0022514cc0a34221286892e5bb"}}, "title": "Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data.", "authors": [{"family": "Yones", "given": "Sara A", "initials": "SA", "orcid": "0000-0002-7201-2604", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1db6ae5db964f149ffc93ea78561711.json"}}, {"family": "Annett", "given": "Alva", "initials": "A"}, {"family": "Stoll", "given": "Patricia", "initials": "P"}, {"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8638ca04ea7f4ff8a191f3c6969b1394.json"}}, {"family": "Holmfeldt", "given": "Linda", "initials": "L", "orcid": "0000-0003-4140-3423", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13a857b0c5b64d10a8e3b6b70d4dc662.json"}}, {"family": "Barren\u00e4s", "given": "Carl Fredrik", "initials": "CF"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f363e8d74594ffeb0d68aa6d774b242.json"}}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1dffb9dd373741069230b4f80d7e1698.json"}}], "type": "journal article", "published": "2022-05-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "7433", "issn-l": "2045-2322"}, "abstract": "Transcriptomic analyses are commonly used to identify differentially expressed genes between patients and controls, or within individuals across disease courses. These methods, whilst effective, cannot encompass the combinatorial effects of genes driving disease. We applied rule-based machine learning (RBML) models and rule networks (RN) to an existing paediatric Systemic Lupus Erythematosus (SLE) blood expression dataset, with the goal of developing gene networks to separate low and high disease activity (DA1 and DA3). The resultant model had an 81% accuracy to distinguish between DA1 and DA3, with unsupervised hierarchical clustering revealing additional subgroups indicative of the immune axis involved or state of disease flare. These subgroups correlated with clinical variables, suggesting that the gene sets identified may further the understanding of gene networks that act in concert to drive disease progression. This included roles for genes (i) induced by interferons (IFI35 and OTOF), (ii) key to SLE cell types (KLRB1 encoding CD161), or (iii) with roles in autophagy and NF-\u03baB pathway responses (CKAP4). As demonstrated here, RBML approaches have the potential to reveal novel gene patterns from within a heterogeneous disease, facilitating patient clinical and therapeutic stratification.", "doi": "10.1038/s41598-022-10853-1", "pmid": "35523803", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9076598"}, {"db": "pii", "key": "10.1038/s41598-022-10853-1"}], "notes": [], "created": "2026-08-20T09:23:25.514Z", "modified": "2026-08-20T09:23:25.697Z"}, {"entity": "publication", "iuid": "3f210f528f12413ba181421bed6f8130", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3f210f528f12413ba181421bed6f8130.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3f210f528f12413ba181421bed6f8130"}}, "title": "Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment.", "authors": [{"family": "Garbulowski", "given": "Mateusz", "initials": "M", "orcid": "0000-0002-2497-194X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/98de355d5a1247cebb494b16444857e6.json"}}, {"family": "Smolinska", "given": "Karolina", "initials": "K", "orcid": "0000-0003-0907-5298", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b491565d0ea04ceb897ce53f325781b3.json"}}, {"family": "\u00c7abuk", "given": "U\u011fur", "initials": "U", "orcid": "0000-0002-4443-3065", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f8ece88ac79e4f4c83714b6b83bcf90c.json"}}, {"family": "Yones", "given": "Sara A", "initials": "SA", "orcid": "0000-0002-7201-2604", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1db6ae5db964f149ffc93ea78561711.json"}}, {"family": "Celli", "given": "Ludovica", "initials": "L", "orcid": "0000-0002-5847-5856", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/914adbe626ea431ab9a30b5b51f3c7b0.json"}}, {"family": "Yaz", "given": "Esma Nur", "initials": "EN"}, {"family": "Barren\u00e4s", "given": "Fredrik", "initials": "F"}, {"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8638ca04ea7f4ff8a191f3c6969b1394.json"}}, {"family": "Wadelius", "given": "Claes", "initials": "C"}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1dffb9dd373741069230b4f80d7e1698.json"}}], "type": "journal article", "published": "2022-02-17", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "14", "issue": "4", "issn-l": "2072-6694"}, "abstract": "Gliomas develop and grow in the brain and central nervous system. Examining glioma grading processes is valuable for improving therapeutic challenges. One of the most extensive repositories storing transcriptomics data for gliomas is The Cancer Genome Atlas (TCGA). However, such big cohorts should be processed with caution and evaluated thoroughly as they can contain batch and other effects. Furthermore, biological mechanisms of cancer contain interactions among biomarkers. Thus, we applied an interpretable machine learning approach to discover such relationships. This type of transparent learning provides not only good predictability, but also reveals co-predictive mechanisms among features. In this study, we corrected the strong and confounded batch effect in the TCGA glioma data. We further used the corrected datasets to perform comprehensive machine learning analysis applied on single-sample gene set enrichment scores using collections from the Molecular Signature Database. Furthermore, using rule-based classifiers, we displayed networks of co-enrichment related to glioma grades. Moreover, we validated our results using the external glioma cohorts. We believe that utilizing corrected glioma cohorts from TCGA may improve the application and validation of any future studies. Finally, the co-enrichment and survival analysis provided detailed explanations for glioma progression and consequently, it should support the targeted treatment.", "doi": "10.3390/cancers14041014", "pmid": "35205761", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8870250"}, {"db": "pii", "key": "cancers14041014"}], "notes": [], "created": "2026-08-20T13:39:39.410Z", "modified": "2026-08-20T13:39:39.667Z"}, {"entity": "publication", "iuid": "e5e18739a37347ed9d1925bb685bcaee", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e5e18739a37347ed9d1925bb685bcaee.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e5e18739a37347ed9d1925bb685bcaee"}}, "title": "Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data", "authors": [{"family": "Yones", "given": "Sara A", "initials": "SA", "orcid": "0000-0002-7201-2604", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1db6ae5db964f149ffc93ea78561711.json"}}, {"family": "Annett", "given": "Alva", "initials": "A"}, {"family": "Stoll", "given": "Patricia", "initials": "P"}, {"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8638ca04ea7f4ff8a191f3c6969b1394.json"}}, {"family": "Holmfeldt", "given": "Linda", "initials": "L", "orcid": "0000-0003-4140-3423", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13a857b0c5b64d10a8e3b6b70d4dc662.json"}}, {"family": "Barren\u00e4s", "given": "Carl Fredrik", "initials": "CF"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f363e8d74594ffeb0d68aa6d774b242.json"}}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1dffb9dd373741069230b4f80d7e1698.json"}}], "type": "posted-content", "published": "2021-06-05", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.06.03.446884", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:04:30.797Z", "modified": "2026-08-20T10:04:30.879Z"}, {"entity": "publication", "iuid": "8561d6585bc748b3bff9999ab15c4e50", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8561d6585bc748b3bff9999ab15c4e50.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8561d6585bc748b3bff9999ab15c4e50"}}, "title": "Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes and normal tissues", "authors": [{"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8638ca04ea7f4ff8a191f3c6969b1394.json"}}, {"family": "Cavalli", "given": "Marco", "initials": "M", "orcid": "0000-0003-1143-1431", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3104b875f2e459093b1e468ba4af556.json"}}, {"family": "Pereira", "given": "Maria J", "initials": "MJ", "orcid": "0000-0001-5498-3899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40667fda2aa5488aa45a95ce4e8a2c1f.json"}}, {"family": "Pan", "given": "Gang", "initials": "G"}, {"family": "Castillejo-Lopez", "given": "Casimiro", "initials": "C"}, {"family": "Kumar", "given": "Chanchal", "initials": "C"}, {"family": "Mundt", "given": "Filip", "initials": "F"}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1dffb9dd373741069230b4f80d7e1698.json"}}, {"family": "Deshmukh", "given": "Atul Shahaji", "initials": "AS", "orcid": "0000-0002-2278-1843", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f87d7b0493d041ca9deb114573a99064.json"}}, {"family": "Mann", "given": "Matthias", "initials": "M", "orcid": "0000-0003-1292-4799", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5dd80d7b355437f9ad1a29efa6814c0.json"}}, {"family": "Korsgren", "given": "Olle", "initials": "O", "orcid": "0000-0002-8524-9547", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4f384eeb31a4b2dba5c9301bb34c156.json"}}, {"family": "Eriksson", "given": "Jan W", "initials": "JW", "orcid": "0000-0002-2639-9481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ddd57ea228848ad9935c38e8b9b64e8.json"}}, {"family": "Wadelius", "given": "Claes", "initials": "C", "orcid": "0000-0002-2033-7829", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f01aa16d2b3343e980a2f2a9eb93af91.json"}}], "type": "posted-content", "published": "2021-05-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.05.09.443296", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:04:08.047Z", "modified": "2026-08-20T10:04:08.243Z"}, {"entity": "publication", "iuid": "84f1b070d44a4a5c851e6269529b32fb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/84f1b070d44a4a5c851e6269529b32fb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/84f1b070d44a4a5c851e6269529b32fb"}}, "title": "Organ-Specific Metabolic Pathways Distinguish Prediabetes, Type 2 Diabetes and Normal Tissues", "authors": [{"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8638ca04ea7f4ff8a191f3c6969b1394.json"}}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Pereira", "given": "Maria J", "initials": "MJ", "orcid": "0000-0001-5498-3899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40667fda2aa5488aa45a95ce4e8a2c1f.json"}}, {"family": "Pan", "given": "Gang", "initials": "G"}, {"family": "Castillejo-L\u00f3pez", "given": "Casimiro", "initials": "C"}, {"family": "Kumar", "given": "Chanchal", "initials": "C"}, {"family": "Mundt", "given": "Filip Oskar", "initials": "FO"}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1dffb9dd373741069230b4f80d7e1698.json"}}, {"family": "Deshmukh", "given": "Atul Shahaji", "initials": "AS", "orcid": "0000-0002-2278-1843", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f87d7b0493d041ca9deb114573a99064.json"}}, {"family": "Mann", "given": "Matthias", "initials": "M"}, {"family": "Korsgren", "given": "Olle", "initials": "O"}, {"family": "Eriksson", "given": "Jan W", "initials": "JW", "orcid": "0000-0002-2639-9481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ddd57ea228848ad9935c38e8b9b64e8.json"}}, {"family": "Wadelius", "given": "Claes", "initials": "C"}], "type": "posted-content", "published": "2021-00-00", "journal": {"issn-l": null}, "abstract": null, "doi": "10.2139/ssrn.3850375", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:01:03.580Z", "modified": "2026-08-20T13:01:03.619Z"}, {"entity": "publication", "iuid": "c6254cf434d948dbbf60007a496740b5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c6254cf434d948dbbf60007a496740b5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c6254cf434d948dbbf60007a496740b5"}}, "title": "Author Correction: Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes.", "authors": [{"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8638ca04ea7f4ff8a191f3c6969b1394.json"}}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Pan", "given": "Gang", "initials": "G"}, {"family": "Pereira", "given": "Maria J", "initials": "MJ", "orcid": "0000-0001-5498-3899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40667fda2aa5488aa45a95ce4e8a2c1f.json"}}, {"family": "Kumar", "given": "Chanchal", "initials": "C"}, {"family": "Skrtic", "given": "Stanko", "initials": "S"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Ris\u00e9rus", "given": "Ulf", "initials": "U"}, {"family": "Eriksson", "given": "Jan W", "initials": "JW"}, {"family": "Komorowski", "given": "Jan", "initials": "J"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}], "type": "published erratum", "published": "2019-11-28", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "18158", "issn-l": "2045-2322"}, "abstract": "An amendment to this paper has been published and can be accessed via a link at the top of the paper.", "doi": "10.1038/s41598-019-54423-4", "pmid": "31776441", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6881403"}, {"db": "pii", "key": "10.1038/s41598-019-54423-4"}], "notes": [], "created": "2026-08-20T09:04:43.916Z", "modified": "2026-08-20T09:04:44.065Z"}, {"entity": "publication", "iuid": "9c3e16b8b897461ab1f8bc81ff7e4db2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9c3e16b8b897461ab1f8bc81ff7e4db2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9c3e16b8b897461ab1f8bc81ff7e4db2"}}, "title": "Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type-2 diabetes", "authors": [{"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8638ca04ea7f4ff8a191f3c6969b1394.json"}}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Pan", "given": "Gang", "initials": "G"}, {"family": "Pereira", "given": "Maria J", "initials": "MJ"}, {"family": "Kumar", "given": "Chanchal", "initials": "C"}, {"family": "Skrtic", "given": "Stanko", "initials": "S"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Ris\u00e9rus", "given": "Ulf", "initials": "U"}, {"family": "Eriksson", "given": "Jan W", "initials": "JW"}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1dffb9dd373741069230b4f80d7e1698.json"}}, {"family": "Wadelius", "given": "Claes", "initials": "C", "orcid": "0000-0002-2033-7829", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f01aa16d2b3343e980a2f2a9eb93af91.json"}}], "type": "posted-content", "published": "2018-09-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/413203", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:11:07.526Z", "modified": "2026-08-20T11:11:07.597Z"}, {"entity": "publication", "iuid": "596c6842840d44b2a37aa630556f1a11", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/596c6842840d44b2a37aa630556f1a11.json"}, "display": {"href": 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