{"entity": "researcher", "timestamp": "2026-08-15T12:48:45.039Z", "family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "affiliations": ["Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.", "Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3"}}, "publications": [{"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", "orcid": "0000-0001-5834-4533", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fcd41a9a3645c3b733564c99a97aea.json"}}, {"family": "Turkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbae52c6a22f4877b747a4de1ec1ca8a.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e85f6d287ce4c60a7b35b287efb4f79.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}], "type": "journal article", "published": "2026-07-00", "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": "2026-06-30T09:59:57.743Z"}, {"entity": "publication", "iuid": "20400326c0944ebda6e786a24f339e26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20400326c0944ebda6e786a24f339e26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20400326c0944ebda6e786a24f339e26"}}, "title": "A human pan-disease blood atlas of the circulating proteome.", "authors": [{"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": 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"https://publications.scilifelab.se/researcher/66bfc091e8784259bfbf0f30a996391e.json"}}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A", "orcid": "0000-0001-8928-3374", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b2d7f254c57489da8329627d49bad87.json"}}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a9c8e243994dccb4730266b0431d6d.json"}}, {"family": "Str\u00e5lin", "given": "Kristoffer", "initials": "K", "orcid": "0000-0002-8801-3169", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6ffa1185f4142b7ab7c372c0c139df6.json"}}, {"family": "Sund\u00e9n-Cullberg", "given": "Jonas", "initials": "J"}, {"family": "Sundling", "given": "Christopher", "initials": "C", "orcid": "0000-0002-6138-690X", "researcher": {"href": "https://publications.scilifelab.se/researcher/89c1e689a46b4b14adb0dc99e1c0a58c.json"}}, {"family": "Sutantiwanichkul", "given": "Thanadol", "initials": "T", "orcid": "0000-0002-1072-6863", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f33fff56f34d72bb1bbc88608ed914.json"}}, {"family": "Svedman", "given": "Fernanda Costa", "initials": "FC", "orcid": "0000-0001-8065-3375", "researcher": {"href": "https://publications.scilifelab.se/researcher/468b2e407aeb49a88b1ef0f7b1e02ce7.json"}}, {"family": "Svensson", "given": "Mattias", "initials": "M", "orcid": "0000-0003-1695-7934", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e3185cf86534a96983b39dd93df454a.json"}}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Tran-Minh", "given": "Khue Hua", "initials": "KH", "orcid": "0000-0002-8964-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/a94e99b0020f4ef28c00bb20e1a1c8ac.json"}}, {"family": "T\u00fcrkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbae52c6a22f4877b747a4de1ec1ca8a.json"}}, {"family": "Unge", "given": "Christian", "initials": "C"}, {"family": "Venge", "given": "Per", "initials": "P", "orcid": "0000-0001-5863-790X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1695020d4d724ba8b378c992e28e21b1.json"}}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}, {"family": "Woessmann", "given": "Jakob", "initials": "J", "orcid": "0000-0002-2283-7237", "researcher": {"href": "https://publications.scilifelab.se/researcher/18460524ba914a91ad61dd2ec231c3a7.json"}}, {"family": "Yang", "given": "Hong", "initials": "H", "orcid": "0009-0002-0414-2471", "researcher": {"href": "https://publications.scilifelab.se/researcher/b52bdf7cbd1745e3a4578f17322c83f1.json"}}, {"family": "Ye\u015filkaya", "given": "Umit Haluk", "initials": "UH"}, {"family": "Yuan", "given": "Meng", "initials": "M", "orcid": "0000-0002-9248-3294", "researcher": {"href": "https://publications.scilifelab.se/researcher/befeb12cfba142eb9dadf81497d6c419.json"}}, {"family": "Zeybel", "given": "Mujdat", "initials": "M", "orcid": "0000-0001-5440-4623", "researcher": {"href": "https://publications.scilifelab.se/researcher/0559b83985134a0a9283ea39601a95a7.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2025-10-09", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": null, "issue": null, "pages": "eadx2678"}, "abstract": "The human blood proteome provides a holistic readout of health states through the assessment of thousands of circulating proteins. Here, we present a pan-disease resource to enable the study of diverse disease phenotypes within a harmonized proteomics dataset. By profiling protein concentrations across 59 diseases and healthy cohorts, we identified proteins associated with age, sex, and BMI, as well as disease-specific signatures. This study highlights shared and distinct protein patterns across conditions, demonstrating the power of a unified proteomics approach to uncover biological insights. The dataset, covering 8,262 individuals and up to 5,416 proteins, serves as an online resource for exploring disease-specific protein profiles and advancing precision medicine research.", "doi": "10.1126/science.adx2678", "pmid": "41066540", "labels": {"Autoimmunity and Serology Profiling": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Proteomics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-10-10T10:37:22.942Z", "modified": "2025-11-07T07:45:07.446Z"}, {"entity": "publication", "iuid": "d9e41b0ebd4d4c0f863ca1f45ef267cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9e41b0ebd4d4c0f863ca1f45ef267cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9e41b0ebd4d4c0f863ca1f45ef267cd"}}, "title": "Systematically identification of survival-associated eQTLs in a Japanese kidney cancer cohort.", "authors": [{"family": "Song", "given": "Xiya", "initials": "X"}, {"family": "Jin", "given": "Han", "initials": "H"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Yuan", "given": "Meng", "initials": "M"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Sato", "given": "Yusuke", "initials": "Y"}, {"family": "Kume", "given": "Haruki", "initials": "H"}, {"family": "Ogawa", "given": "Seishi", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "21", "issue": "7", "pages": "e1011770", "issn-l": "1553-7390"}, "abstract": "Clear cell renal carcinoma (ccRCC) is the predominant form of kidney cancer, but the prognostic value of expression quantitative trait loci (eQTLs) remains underexplored, particularly in Asian populations.\n\nWe analyzed whole-exome sequencing and RNA sequencing data from 100 Japanese ccRCC patients to identify eQTLs. Multiple Cox proportional hazard models assessed survival associations, with validation in the Cancer Genome Atlas ccRCC cohort (n = 287).\n\nWe identified 805 eGenes and 4,558 cis-eQTLs in the Japanese cohort. Survival analysis revealed a total of 9 eGenes significantly associated with overall survival (FDR < 0.05). Further exploratory analysis were performed using 158 eGenes and 711 eQTLs (p-value <0.05) as potential prognostic signals. Among these, 223 eQTLs regulating 54 eGenes showed consistent prognostic effects at both expression and genetic levels. Cross-population validation identified eight eQTLs regulating 11 eGenes with reproducible survival associations across ethnicities, including a missense mutation in ERV3-1 and regulatory variants near ANKRD20A7P. These variants demonstrated consistent allelic effects on both gene expression and patient survival in both cohorts.", "doi": "10.1371/journal.pgen.1011770", "pmid": "40622919", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12233309"}, {"db": "pii", "key": "PGENETICS-D-25-00018"}], "notes": [], "created": "2025-11-28T10:53:53.218Z", "modified": "2025-11-28T10:53:53.295Z"}, {"entity": "publication", "iuid": "59c6a9db7d8d4f358f854245b00ff172", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59c6a9db7d8d4f358f854245b00ff172.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59c6a9db7d8d4f358f854245b00ff172"}}, "title": "Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats.", "authors": [{"family": "Yang", "given": "Hong", "initials": "H", "orcid": "0009-0002-0414-2471", "researcher": {"href": "https://publications.scilifelab.se/researcher/b52bdf7cbd1745e3a4578f17322c83f1.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Shi", "given": "Mengnan", "initials": "M"}, {"family": "Kiliclioglu", "given": "Metin", "initials": "M"}, {"family": "Bayram", "given": "Cemil", "initials": "C"}, {"family": "Bolar", "given": "Ismail", "initials": "I"}, {"family": "Tozlu", "given": "\u00d6zlem \u00d6zdemir", "initials": "\u00d6\u00d6"}, {"family": "Baba", "given": "Cem", "initials": "C"}, {"family": "Yuksel", "given": "Nursena", "initials": "N"}, {"family": "Yildirim", "given": "Serkan", "initials": "S"}, {"family": "Iqbal", "given": "Shazia", "initials": "S"}, {"family": "Sebhaoui", "given": "Jihad", "initials": "J"}, {"family": "Hac\u0131muftuoglu", "given": "Ahmet", "initials": "A"}, {"family": "Uhlen", "given": "Matthias", "initials": "M"}, {"family": "Boren", "given": "Jan", "initials": "J"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}], "type": "journal article", "published": "2025-02-11", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "13", "issn-l": "2050-084X"}, "abstract": "Excessive consumption of sucrose, in the form of sugar-sweetened beverages, has been implicated in the pathogenesis of metabolic dysfunction-associated fatty liver disease (MAFLD) and other related metabolic syndromes. The c-Jun N-terminal kinase (JNK) pathway plays a crucial role in response to dietary stressors, and it was demonstrated that the inhibition of the JNK pathway could potentially be used in the treatment of MAFLD. However, the intricate mechanisms underlying these interventions remain incompletely understood given their multifaceted effects across multiple tissues. In this study, we challenged rats with sucrose-sweetened water and investigated the potential effects of JNK inhibition by employing network analysis based on the transcriptome profiling obtained from hepatic and extrahepatic tissues, including visceral white adipose tissue, skeletal muscle, and brain. Our data demonstrate that JNK inhibition by JNK-IN-5A effectively reduces the circulating triglyceride accumulation and inflammation in rats subjected to sucrose consumption. Coexpression analysis and genome-scale metabolic modeling reveal that sucrose overconsumption primarily induces transcriptional dysfunction related to fatty acid and oxidative metabolism in the liver and adipose tissues, which are largely rectified after JNK inhibition at a clinically relevant dose. Skeletal muscle exhibited minimal transcriptional changes to sucrose overconsumption but underwent substantial metabolic adaptation following the JNK inhibition. Overall, our data provides novel insights into the molecular basis by which JNK inhibition exerts its metabolic effect in the metabolically active tissues. Furthermore, our findings underpin the critical role of extrahepatic metabolism in the development of diet-induced steatosis, offering valuable guidance for future studies focused on JNK-targeting for effective treatment of MAFLD.", "doi": "10.7554/eLife.98427", "pmid": "39932177", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11813226"}, {"db": "pii", "key": "98427"}, {"db": "GEO", "key": "GSE282954"}], "notes": [], "created": "2025-11-28T10:54:50.019Z", "modified": "2025-11-28T10:54:50.040Z"}, {"entity": "publication", "iuid": "e20232eba3084478a0d4cb3b52b4a953", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e20232eba3084478a0d4cb3b52b4a953.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e20232eba3084478a0d4cb3b52b4a953"}}, "title": "Transient colonizing microbes promote gut dysbiosis and functional impairment.", "authors": [{"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Meslier", "given": "Victoria", "initials": "V", "orcid": "0000-0003-2699-0092", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cd1d7bc18954f988d1e3f5200e124eb.json"}}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G"}, {"family": "Garcia-Guevara", "given": "Fernando", "initials": "F"}, {"family": "Etienne-Mesmin", "given": "Lucie", "initials": "L", "orcid": "0000-0001-6104-6043", "researcher": {"href": "https://publications.scilifelab.se/researcher/51e9e5819e4e43b08593df4c66c1f0b3.json"}}, {"family": "Clasen", "given": "Frederick", "initials": "F"}, {"family": "Park", "given": "Junseok", "initials": "J", "orcid": "0000-0003-2312-9440", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5b77f5a5b98479db82a0790affe0a46.json"}}, {"family": "Plaza O\u00f1ate", "given": "Florian", "initials": "F", "orcid": "0000-0001-6036-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a2a015ed8dd47f29f37ef700ccf65d0.json"}}, {"family": "Cai", "given": "Haizhuang", "initials": "H"}, {"family": "Le Chatelier", "given": "Emmanuelle", "initials": "E", "orcid": "0000-0002-2724-0536", "researcher": {"href": "https://publications.scilifelab.se/researcher/99c1ea4535d24ffca619adc5e54b5e80.json"}}, {"family": "Pons", "given": "Nicolas", "initials": "N"}, {"family": "Pereira", "given": "Marcela", "initials": "M"}, {"family": "Seifert", "given": "Maike", "initials": "M"}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications.scilifelab.se/researcher/514fbe8cab5e4f25afa33fcd3e0523b5.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Lee", "given": "Doheon", "initials": "D", "orcid": "0000-0001-9070-4316", "researcher": {"href": "https://publications.scilifelab.se/researcher/766833afa7534fb68e04525078040b65.json"}}, {"family": "Proctor", "given": "Gordon", "initials": "G", "orcid": "0000-0002-5684-841X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d55a1e72dd9444239c5054ccf7876be3.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Blanquet-Diot", "given": "St\u00e9phanie", "initials": "S", "orcid": "0000-0003-0692-8726", "researcher": {"href": "https://publications.scilifelab.se/researcher/0689cb23d6fa472aab4623c4c8e611db.json"}}, {"family": "Moyes", "given": "David", "initials": "D", "orcid": "0000-0002-1657-918X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a6f9404ad0b420bb54962af7f9ff2f5.json"}}, {"family": "Almeida", "given": "Mathieu", "initials": "M", "orcid": "0000-0003-4971-0049", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cbbdb8b00b84a33a862ef1f8f030555.json"}}, {"family": "Ehrlich", "given": "S Dusko", "initials": "SD"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Shoaie", "given": "Saeed", "initials": "S", "orcid": "0000-0001-5834-4533", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fcd41a9a3645c3b733564c99a97aea.json"}}], "type": "journal article", "published": "2024-09-08", "journal": {"title": "NPJ Biofilms Microbiomes", "issn": "2055-5008", "volume": "10", "issue": "1", "pages": "80", "issn-l": "2055-5008"}, "abstract": "Species composition of the healthy adult gut microbiota tends to be stable over time. Destabilization of the gut microbiome under the influence of different factors is the main driver of the microbial dysbiosis and subsequent impacts on host physiology. Here, we used metagenomics data from a Swedish longitudinal cohort, to determine the stability of the gut microbiome and uncovered two distinct microbial species groups; persistent colonizing species (PCS) and transient colonizing species (TCS). We validated the continuation of this grouping, generating gut metagenomics data for additional time points from the same Swedish cohort. We evaluated the existence of PCS/TCS across different geographical regions and observed they are globally conserved features. To characterize PCS/TCS phenotypes, we performed bioreactor fermentation with faecal samples and metabolic modeling. Finally, using chronic disease gut metagenome and other multi-omics data, we identified roles of TCS in microbial dysbiosis and link with abnormal changes to host physiology.", "doi": "10.1038/s41522-024-00561-1", "pmid": "39245657", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11381545"}, {"db": "pii", "key": "10.1038/s41522-024-00561-1"}], "notes": [], "created": "2024-11-25T10:18:41.173Z", "modified": "2025-02-28T14:15:02.782Z"}, {"entity": "publication", "iuid": "4f8d564f67734ecb989124d50507c8da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f8d564f67734ecb989124d50507c8da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f8d564f67734ecb989124d50507c8da"}}, "title": "Combined Metabolic Activators with Different NAD+ Precursors Improve Metabolic Functions in the Animal Models of Neurodegenerative Diseases.", "authors": [{"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Yildirim", "given": "Serkan", "initials": "S", "orcid": "0000-0003-2457-3367", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ca45645b9734857b37821c08845060b.json"}}, {"family": "Bayram", "given": "Cemil", "initials": "C"}, {"family": "Bolat", "given": "Ismail", "initials": "I"}, {"family": "Oner", "given": "Sena", "initials": "S"}, {"family": "Tozlu", "given": "Ozlem Ozdemir", "initials": "OO", "orcid": "0000-0002-5472-8174", "researcher": {"href": "https://publications.scilifelab.se/researcher/56f7d9ec801d4a91a32aa1c8ff999c74.json"}}, {"family": "Arslan", "given": "Mehmet Enes", "initials": "ME", "orcid": "0000-0002-1600-2305", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8de47fe6c1644919ab4ea1f5aca098b.json"}}, {"family": "Hacimuftuoglu", "given": "Ahmet", "initials": "A"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e85f6d287ce4c60a7b35b287efb4f79.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Turkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbae52c6a22f4877b747a4de1ec1ca8a.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}], "type": "journal article", "published": "2024-04-22", "journal": {"title": "Biomedicines", "issn": "2227-9059", "volume": "12", "issue": "4", "issn-l": null}, "abstract": "Mitochondrial dysfunction and metabolic abnormalities are acknowledged as significant factors in the onset of neurodegenerative disorders such as Parkinson's disease (PD) and Alzheimer's disease (AD). Our research has demonstrated that the use of combined metabolic activators (CMA) may alleviate metabolic dysfunctions and stimulate mitochondrial metabolism. Therefore, the use of CMA could potentially be an effective therapeutic strategy to slow down or halt the progression of PD and AD. CMAs include substances such as the glutathione precursors (L-serine and N-acetyl cysteine), the NAD+ precursor (nicotinamide riboside), and L-carnitine tartrate.\n\nHere, we tested the effect of two different formulations, including CMA1 (nicotinamide riboside, L-serine, N-acetyl cysteine, L-carnitine tartrate), and CMA2 (nicotinamide, L-serine, N-acetyl cysteine, L-carnitine tartrate), as well as their individual components, on the animal models of AD and PD. We assessed the brain and liver tissues for pathological changes and immunohistochemical markers. Additionally, in the case of PD, we performed behavioral tests and measured responses to apomorphine-induced rotations.\n\nHistological analysis showed that the administration of both CMA1 and CMA2 formulations led to improvements in hyperemia, degeneration, and necrosis in neurons for both AD and PD models. Moreover, the administration of CMA2 showed a superior effect compared to CMA1. This was further corroborated by immunohistochemical data, which indicated a reduction in immunoreactivity in the neurons. Additionally, notable metabolic enhancements in liver tissues were observed using both formulations. In PD rat models, the administration of both formulations positively influenced the behavioral functions of the animals.\n\nOur findings suggest that the administration of both CMA1 and CMA2 markedly enhanced metabolic and behavioral outcomes, aligning with neuro-histological observations. These findings underscore the promise of CMA2 administration as an effective therapeutic strategy for enhancing metabolic parameters and cognitive function in AD and PD patients.", "doi": "10.3390/biomedicines12040927", "pmid": "38672280", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11048203"}, {"db": "pii", "key": "biomedicines12040927"}], "notes": [], "created": "2024-11-25T10:33:35.720Z", "modified": "2025-02-28T14:24:33.584Z"}, {"entity": "publication", "iuid": "bd7e4686333d489495edae6e2cb9e54a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd7e4686333d489495edae6e2cb9e54a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd7e4686333d489495edae6e2cb9e54a"}}, "title": "Next generation pan-cancer blood proteome profiling using proximity extension assay.", "authors": [{"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd5ff31463cd4345a1fc8351e797ac7f.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Lundin", "given": "Emma", "initials": "E", "orcid": "0009-0000-7711-1962", "researcher": {"href": "https://publications.scilifelab.se/researcher/06761839da88443e9098d9562810fb7f.json"}}, {"family": "Rameika", "given": "Natallia", "initials": "N", "orcid": "0000-0002-7835-4357", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a1b2d0ce6ea452b82a35c603a073eb1.json"}}, {"family": "Enblad", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-0594-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/11313af3f4a241ecb93af23ab2652195.json"}}, {"family": "Lindman", "given": "Henrik", "initials": "H"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M", "orcid": "0000-0003-2468-0226", "researcher": {"href": "https://publications.scilifelab.se/researcher/8717164448ee4e2797fefd365103ddc8.json"}}, {"family": "Hesselager", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-9613-1344", "researcher": {"href": "https://publications.scilifelab.se/researcher/978fc6fea7d54f5b81a8b5a87efa083a.json"}}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a9c8e243994dccb4730266b0431d6d.json"}}, {"family": "Enblad", "given": "Malin", "initials": "M", "orcid": "0000-0001-5900-0900", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e801966db544e6286fb2b4037980dba.json"}}, {"family": "Simonson", "given": "Oscar E", "initials": "OE", "orcid": "0000-0002-3552-5558", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a52b4426da84787aeb56b8d6232ba87.json"}}, {"family": "H\u00e4ggman", "given": "Michael", "initials": "M"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2023-07-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "4308"}, "abstract": "A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.", "doi": "10.1038/s41467-023-39765-y", "pmid": "37463882", "labels": {"Affinity Proteomics Uppsala": "Collaborative", "NGI Proteomics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10354027"}, {"db": "pii", "key": "10.1038/s41467-023-39765-y"}], "notes": [], "created": "2023-11-29T19:16:18.991Z", "modified": "2024-01-16T13:48:32.880Z"}, {"entity": "publication", "iuid": "c49e0cc35a87422684626d3380052c2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c49e0cc35a87422684626d3380052c2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c49e0cc35a87422684626d3380052c2e"}}, "title": "Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis.", "authors": [{"family": "Zeybel", "given": "Mujdat", "initials": "M"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Shi", "given": "Mengnan", "initials": "M"}, {"family": "Akyildiz", "given": "Murat", "initials": "M"}, {"family": "Saglam", "given": "Burcin", "initials": "B"}, {"family": "Gonenli", "given": "Mehmet Gokhan", "initials": "MG"}, {"family": "Yigit", "given": "Buket", "initials": "B"}, {"family": "Ulukan", "given": "Burge", "initials": "B"}, {"family": "Ural", "given": "Dilek", "initials": "D"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "Adv Sci (Weinh)", "issn": "2198-3844", "volume": "9", "issue": "11", "pages": "e2104373", "issn-l": null}, "abstract": "Metabolic dysfunction-associated fatty liver disease (MAFLD) is a complex disease involving alterations in multiple biological processes regulated by the interactions between obesity, genetic background, and environmental factors including the microbiome. To decipher hepatic steatosis (HS) pathogenesis by excluding critical confounding factors including genetic variants and diabetes, 56 heterogenous MAFLD patients are characterized by generating multiomics data including oral and gut metagenomics as well as plasma metabolomics and inflammatory proteomics data. The dysbiosis in the oral and gut microbiome is explored and the host-microbiome interactions based on global metabolic and inflammatory processes are revealed. These multiomics data are integrated using the biological network and HS's key features are identified using multiomics data. HS is finally predicted using these key features and findings are validated in a follow-up cohort, where 22 subjects with varying degree of HS are characterized.", "doi": "10.1002/advs.202104373", "pmid": "35128832", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9008426"}], "notes": [], "created": "2022-11-11T06:30:03.753Z", "modified": "2022-11-11T06:30:03.759Z"}, {"entity": "publication", "iuid": "9cf991afbb304011966f1c8a15903e45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9cf991afbb304011966f1c8a15903e45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9cf991afbb304011966f1c8a15903e45"}}, "title": "Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients.", "authors": [{"family": "Zeybel", "given": "Mujdat", "initials": "M"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Fredolini", "given": "Claudia", "initials": "C"}, {"family": "Akyildiz", "given": "Murat", "initials": "M"}, {"family": "Saglam", "given": "Burcin", "initials": "B"}, {"family": "Gonenli", "given": "Mehmet Gokhan", "initials": "MG", "orcid": "0000-0003-2925-7048", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc46a0ff3f5d4b5bbb890e816a93f921.json"}}, {"family": "Ural", "given": "Dilek", "initials": "D", "orcid": "0000-0003-0224-1433", "researcher": {"href": "https://publications.scilifelab.se/researcher/8013cf660d6044faa819113f3a80906a.json"}}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e85f6d287ce4c60a7b35b287efb4f79.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "Mol. Syst. Biol.", "issn": "1744-4292", "issn-l": "1744-4292", "volume": "17", "issue": "10", "pages": "e10459"}, "abstract": "Nonalcoholic fatty liver disease (NAFLD) refers to excess fat accumulation in the liver. In animal experiments and human kinetic study, we found that administration of combined metabolic activators (CMAs) promotes the oxidation of fat, attenuates the resulting oxidative stress, activates mitochondria, and eventually removes excess fat from the liver. Here, we tested the safety and efficacy of CMA in NAFLD patients in a placebo-controlled 10-week study. We found that CMA significantly decreased hepatic steatosis and levels of aspartate aminotransferase, alanine aminotransferase, uric acid, and creatinine, whereas found no differences on these variables in the placebo group after adjustment for weight loss. By integrating clinical data with plasma metabolomics and inflammatory proteomics as well as oral and gut metagenomic data, we revealed the underlying molecular mechanisms associated with the reduced hepatic fat and inflammation in NAFLD patients and identified the key players involved in the host-microbiome interactions. In conclusion, we showed that CMA can be used to develop a pharmacological treatment strategy in NAFLD patients.", "doi": "10.15252/msb.202110459", "pmid": "34694070", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-12-06T07:41:32.157Z", "modified": "2021-12-09T13:49:24.870Z"}, {"entity": "publication", "iuid": "33c8e19f612e4870b5d7b392ab1d37ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33c8e19f612e4870b5d7b392ab1d37ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33c8e19f612e4870b5d7b392ab1d37ff"}}, "title": "Combined Metabolic Activators Accelerates Recovery in Mild-to-Moderate COVID-19.", "authors": [{"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Ayd\u0131n", "given": "Mehtap", "initials": "M"}, {"family": "Alkurt", "given": "Gizem", "initials": "G"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Akyol", "given": "Dogukan", "initials": "D"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Dinler-Doganay", "given": "Gizem", "initials": "G"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Olmuscelik", "given": "Oktay", "initials": "O"}, {"family": "Doganay", "given": "Levent", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}], "type": "clinical trial, phase ii", "published": "2021-09-00", "journal": {"title": "Adv Sci (Weinh)", "issn": "2198-3844", "issn-l": null, "volume": "8", "issue": "17", "pages": "e2101222"}, "abstract": "COVID-19 is associated with mitochondrial dysfunction and metabolic abnormalities, including the deficiencies in nicotinamide adenine dinucleotide (NAD+ ) and glutathione metabolism. Here it is investigated if administration of a mixture of combined metabolic activators (CMAs) consisting of glutathione and NAD+ precursors can restore metabolic function and thus aid the recovery of COVID-19 patients. CMAs include l-serine, N-acetyl-l-cysteine, nicotinamide riboside, and l-carnitine tartrate, salt form of l-carnitine. Placebo-controlled, open-label phase 2 study and double-blinded phase 3 clinical trials are conducted to investigate the time of symptom-free recovery on ambulatory patients using CMAs. The results of both studies show that the time to complete recovery is significantly shorter in the CMA group (6.6 vs 9.3 d) in phase 2 and (5.7 vs 9.2 d) in phase 3 trials compared to placebo group. A comprehensive analysis of the plasma metabolome and proteome reveals major metabolic changes. Plasma levels of proteins and metabolites associated with inflammation and antioxidant metabolism are significantly improved in patients treated with CMAs as compared to placebo. The results show that treating patients infected with COVID-19 with CMAs lead to a more rapid symptom-free recovery, suggesting a role for such a therapeutic regime in the treatment of infections leading to respiratory problems.", "doi": "10.1002/advs.202101222", "pmid": "34180141", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8420376"}], "notes": [], "created": "2021-10-06T10:54:39.324Z", "modified": "2021-12-09T13:48:15.216Z"}, {"entity": "publication", "iuid": "cee69667064f4aa186925651c58a42f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cee69667064f4aa186925651c58a42f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cee69667064f4aa186925651c58a42f9"}}, "title": "A single-cell type transcriptomics map of human tissues.", "authors": [{"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "M\u00e9ar", "given": "Loren", "initials": "L", "orcid": "0000-0001-9333-0110", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4f441a799324599953796b467abf95c.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Digre", "given": "Andreas", "initials": "A", "orcid": "0000-0003-1145-6700", "researcher": {"href": "https://publications.scilifelab.se/researcher/b83918be53c64470a67ab23170b86b11.json"}}, {"family": "Katona", "given": "Borbala", "initials": "B"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Butler", "given": "Lynn", "initials": "L"}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Dusart", "given": "Philip", "initials": "P"}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Li", "given": "Xiangyu", "initials": "X", "orcid": "0000-0002-8301-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c15b68f3b7f4188b9927c011d586efd.json"}}, {"family": "Ozcan", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-1222-2802", "researcher": {"href": "https://publications.scilifelab.se/researcher/480be47a6ccd4f9ebc66d718997a3462.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}, {"family": "Luo", "given": "Yonglun", "initials": "Y", "orcid": "0000-0002-0007-7759", "researcher": {"href": "https://publications.scilifelab.se/researcher/0aad9ec706674ed6ab358a445ba1989d.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "31", "pages": "eabh2169", "issn-l": "2375-2548"}, "abstract": "Advances in molecular profiling have opened up the possibility to map the expression of genes in cells, tissues, and organs in the human body. Here, we combined single-cell transcriptomics analysis with spatial antibody-based protein profiling to create a high-resolution single-cell type map of human tissues. An open access atlas has been launched to allow researchers to explore the expression of human protein-coding genes in 192 individual cell type clusters. An expression specificity classification was performed to determine the number of genes elevated in each cell type, allowing comparisons with bulk transcriptomics data. The analysis highlights distinct expression clusters corresponding to cell types sharing similar functions, both within the same organs and between organs.", "doi": "10.1126/sciadv.abh2169", "pmid": "34321199", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "7/31/eabh2169"}, {"db": "pmc", "key": "PMC8318366"}], "notes": [], "created": "2021-08-27T07:22:02.009Z", "modified": "2024-01-16T13:48:39.387Z"}, {"entity": "publication", "iuid": "043ab27fa61944e99a7e279442373b57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/043ab27fa61944e99a7e279442373b57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/043ab27fa61944e99a7e279442373b57"}}, "title": "Integration of molecular profiles in a longitudinal wellness profiling cohort.", "authors": [{"family": "Tebani", "given": "Abdellah", "initials": "A"}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb164de27f2846328bb675876922a5fe.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Koistinen", "given": "Ina Schuppe", "initials": "IS"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Olsson", "given": "Lisa M", "initials": "LM", "orcid": "0000-0001-9730-1915", "researcher": {"href": "https://publications.scilifelab.se/researcher/2460963d77ee4eee9409fbd8c257d910.json"}}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications.scilifelab.se/researcher/514fbe8cab5e4f25afa33fcd3e0523b5.json"}}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Stenlund", "given": "Hans", "initials": "H"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-0880-5375", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbf3f75938f0442a9b1ae5c98565f44a.json"}}, {"family": "Karlsson", "given": "Max J", "initials": "MJ", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf18af5b676b449693945249fc1767e4.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Olin", "given": "Axel", "initials": "A", "orcid": "0000-0002-1161-4476", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dfb8efde80a4a508c93714729259aba.json"}}, {"family": "Mikes", "given": "Jaromir", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "Danielsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6959-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e346ce0d514179baea3c97b615e665.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Jansson", "given": "Per-Anders", "initials": "PA"}, {"family": "Anger\u00e5s", "given": "Oskar", "initials": "O"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Kjellqvist", "given": "Sanela", "initials": "S"}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Moritz", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4258-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/95ad5b7fe48f42eda1328f54a385e097.json"}}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-4871-8818", "researcher": {"href": "https://publications.scilifelab.se/researcher/1689878e0c5542d08d3e2d5043a6ce5c.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4289-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbc3ade3079e4265ad42ed1be485bc24.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}], "type": "journal article", "published": "2020-09-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "4487"}, "abstract": "An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies and immune cell profiling, complemented with gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine.", "doi": "10.1038/s41467-020-18148-7", "pmid": "32900998", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Autoimmunity and Serology Profiling": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative", "Cellular Immunomonitoring": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-18148-7"}, {"db": "pmc", "key": "PMC7479148"}], "notes": [], "created": "2020-09-10T05:17:29.818Z", "modified": "2025-10-17T13:03:16.662Z"}, {"entity": "publication", "iuid": "f4135a8deebe4537aedfb6f14b11712e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4135a8deebe4537aedfb6f14b11712e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4135a8deebe4537aedfb6f14b11712e"}}, "title": "The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non-alcoholic fatty liver disease.", "authors": [{"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Bjornson", "given": "Elias", "initials": "E"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Tebani", "given": "Abdellah", "initials": "A", "orcid": "0000-0002-8901-2678", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf47745ed3454f3c819cf6414f140ff0.json"}}, {"family": "Lovric", "given": "Alen", "initials": "A"}, {"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca09f57bdc44e7fa33a472f04859a4d.json"}}, {"family": "Ozcan", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-1222-2802", "researcher": {"href": "https://publications.scilifelab.se/researcher/480be47a6ccd4f9ebc66d718997a3462.json"}}, {"family": "Juszczak", "given": "Kajetan", "initials": "K"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Kim", "given": "Jung Tae", "initials": "JT"}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G"}, {"family": "St\u00e5hlman", "given": "Marcus", "initials": "M"}, {"family": "Bergh", "given": "Per-Olof", "initials": "PO", "orcid": "0000-0001-9993-6965", "researcher": {"href": "https://publications.scilifelab.se/researcher/28c1f37dc6cc4ed98c8e8eb1a621fa2c.json"}}, {"family": "Adiels", "given": "Martin", "initials": "M"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Taskinen", "given": "Marja-Riitta", "initials": "MR"}, {"family": "Bosley", "given": "Jim", "initials": "J"}, {"family": "Marschall", "given": "Hanns-Ulrich", "initials": "HU"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e85f6d287ce4c60a7b35b287efb4f79.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}], "type": "journal article", "published": "2020-04-00", "journal": {"title": "Mol. Syst. Biol.", "issn": "1744-4292", "volume": "16", "issue": "4", "pages": "e9495", "issn-l": "1744-4292"}, "abstract": "The prevalence of non-alcoholic fatty liver disease (NAFLD) continues to increase dramatically, and there is no approved medication for its treatment. Recently, we predicted the underlying molecular mechanisms involved in the progression of NAFLD using network analysis and identified metabolic cofactors that might be beneficial as supplements to decrease human liver fat. Here, we first assessed the tolerability of the combined metabolic cofactors including l-serine, N-acetyl-l-cysteine (NAC), nicotinamide riboside (NR), and l-carnitine by performing a 7-day rat toxicology study. Second, we performed a human calibration study by supplementing combined metabolic cofactors and a control study to study the kinetics of these metabolites in the plasma of healthy subjects with and without supplementation. We measured clinical parameters and observed no immediate side effects. Next, we generated plasma metabolomics and inflammatory protein markers data to reveal the acute changes associated with the supplementation of the metabolic cofactors. We also integrated metabolomics data using personalized genome-scale metabolic modeling and observed that such supplementation significantly affects the global human lipid, amino acid, and antioxidant metabolism. Finally, we predicted blood concentrations of these compounds during daily long-term supplementation by generating an ordinary differential equation model and liver concentrations of serine by generating a pharmacokinetic model and finally adjusted the doses of individual metabolic cofactors for future human clinical trials.", "doi": "10.15252/msb.209495", "pmid": "32337855", "labels": {"Affinity Proteomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7184219"}], "notes": [], "created": "2020-12-10T16:30:05.091Z", "modified": "2024-01-16T13:48:42.677Z"}, {"entity": "publication", "iuid": "36235e9dc3c244d7a5646615de05fe18", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36235e9dc3c244d7a5646615de05fe18.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36235e9dc3c244d7a5646615de05fe18"}}, "title": "An atlas of human metabolism.", "authors": [{"family": "Robinson", "given": "Jonathan L", "initials": "JL", "orcid": "0000-0001-8567-5960", "researcher": {"href": "https://publications.scilifelab.se/researcher/b70b6d9b64fd45e882c4108aded013d4.json"}}, {"family": "Kocaba\u015f", "given": "P\u0131nar", "initials": "P", "orcid": "0000-0001-9788-2019", "researcher": {"href": "https://publications.scilifelab.se/researcher/c89eb03e619945a2a2058179b0d0e310.json"}}, {"family": "Wang", "given": "Hao", "initials": "H", "orcid": "0000-0001-7475-0136", "researcher": {"href": "https://publications.scilifelab.se/researcher/836b4fbf7ebd4f80abc84465c8f29a2e.json"}}, {"family": "Cholley", "given": "Pierre-Etienne", "initials": "PE"}, {"family": "Cook", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5534-8600", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad0b42774a1e4e0580dde05e95fcb1fc.json"}}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications.scilifelab.se/researcher/44da161dba604c9e803a4af303277083.json"}}, {"family": "Anton", "given": "Mihail", "initials": "M", "orcid": "0000-0002-7753-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a28ecc2261e436ea5884ada5e512aed.json"}}, {"family": "Ferreira", "given": "Raphael", "initials": "R", "orcid": "0000-0001-9881-6232", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e97f22759cd4e008d9b6473f52865e5.json"}}, {"family": "Domenzain", "given": "Iv\u00e1n", "initials": "I", "orcid": "0000-0002-5322-2040", "researcher": {"href": "https://publications.scilifelab.se/researcher/3793e87625584ee2a31301297263a12a.json"}}, {"family": "Billa", "given": "Virinchi", "initials": "V"}, {"family": "Limeta", "given": "Angelo", "initials": "A"}, {"family": "Hedin", "given": "Alex", "initials": "A", "orcid": "0000-0002-0829-2496", "researcher": {"href": "https://publications.scilifelab.se/researcher/88756d4d3b894ab288141af7b9c9b052.json"}}, {"family": "Gustafsson", "given": "Johan", "initials": "J", "orcid": "0000-0001-5072-2659", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd5fda1ac79e49c185ba6f4dfcdff5fc.json"}}, {"family": "Kerkhoven", "given": "Eduard J", "initials": "EJ", "orcid": "0000-0002-3593-5792", "researcher": {"href": "https://publications.scilifelab.se/researcher/0df361f8014144e79479631fcbffad53.json"}}, {"family": "Svensson", "given": "L Thomas", "initials": "LT", "orcid": "0000-0002-9190-2979", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc636683ece84dc4ac3e4d10df0c7a49.json"}}, {"family": "Palsson", "given": "Bernhard O", "initials": "BO", "orcid": "0000-0003-2357-6785", "researcher": {"href": "https://publications.scilifelab.se/researcher/b72eed29485a433cb85e260ee38dc894.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Hansson", "given": "Lena", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2020-03-24", "journal": {"title": "Sci Signal", "issn": "1937-9145", "issn-l": "1945-0877", "volume": "13", "issue": "624", "pages": null}, "abstract": "Genome-scale metabolic models (GEMs) are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. Researchers have developed increasingly comprehensive human GEMs, but the disconnect among different model sources and versions impedes further progress. We therefore integrated and extensively curated the most recent human metabolic models to construct a consensus GEM, Human1. We demonstrated the versatility of Human1 through the generation and analysis of cell- and tissue-specific models using transcriptomic, proteomic, and kinetic data. We also present an accompanying web portal, Metabolic Atlas (https://www.metabolicatlas.org/), which facilitates further exploration and visualization of Human1 content. Human1 was created using a version-controlled, open-source model development framework to enable community-driven curation and refinement. This framework allows Human1 to be an evolving shared resource for future studies of human health and disease.", "doi": "10.1126/scisignal.aaz1482", "pmid": "32209698", "labels": {"Systems Biology": "Technology development", "Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pii", "key": "13/624/eaaz1482"}, {"db": "pmc", "key": "PMC7331181"}, {"db": "mid", "key": "NIHMS1590510"}], "notes": [], "created": "2020-12-10T11:11:44.807Z", "modified": "2021-11-10T12:52:52.282Z"}, {"entity": "publication", "iuid": "bb89d24bf5de4738810b72a84a0ad0b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb89d24bf5de4738810b72a84a0ad0b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb89d24bf5de4738810b72a84a0ad0b6"}}, "title": "An atlas of the protein-coding genes in the human, pig, and mouse brain.", "authors": [{"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Mitsios", "given": "Nicholas", "initials": "N", "orcid": "0000-0001-6243-4953", "researcher": {"href": "https://publications.scilifelab.se/researcher/38efa44f5ed64192b432d6384584f00d.json"}}, {"family": "Adori", "given": "Csaba", "initials": "C"}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Limiszewska", "given": "Agnieszka", "initials": "A", "orcid": "0000-0003-1601-8195", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e7b9e0e376422491d8bd1d76d6f774.json"}}, {"family": "Hikmet", "given": "Feria", "initials": "F", "orcid": "0000-0002-3750-9308", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e8c8f511fef466dafd7d704e17d2e30.json"}}, {"family": "Huang", "given": "Jinrong", "initials": "J", "orcid": "0000-0001-8085-9939", "researcher": {"href": "https://publications.scilifelab.se/researcher/00a7eea9544b457b8b058c98e0f4ee94.json"}}, {"family": "Du", "given": "Yutao", "initials": "Y"}, {"family": "Lin", "given": "Lin", "initials": "L", "orcid": "0000-0002-7546-4948", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6436e2b14cd4a629aeebed48b3ae0a9.json"}}, {"family": "Dong", "given": "Zhanying", "initials": "Z"}, {"family": "Yang", "given": "Ling", "initials": "L", "orcid": "0000-0002-5425-8256", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e150be60a3740b89511174e0fd8fa6e.json"}}, {"family": "Liu", "given": "Xin", "initials": "X", "orcid": "0000-0003-3256-2940", "researcher": {"href": "https://publications.scilifelab.se/researcher/b130e21a82a94eb7acd0333f3e62b6ba.json"}}, {"family": "Jiang", "given": "Hui", "initials": "H"}, {"family": "Xu", "given": "Xun", "initials": "X", "orcid": "0000-0002-5338-5173", "researcher": {"href": "https://publications.scilifelab.se/researcher/c96e82115f8d493ea665e5dfe2a374e9.json"}}, {"family": "Wang", "given": "Jian", "initials": "J"}, {"family": "Yang", "given": "Huanming", "initials": "H", "orcid": "0000-0003-1703-3012", "researcher": {"href": "https://publications.scilifelab.se/researcher/6575b8191e414162b52d26df8d9af26a.json"}}, {"family": "Bolund", "given": "Lars", "initials": "L"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Luo", "given": "Yonglun", "initials": "Y", "orcid": "0000-0002-0007-7759", "researcher": {"href": "https://publications.scilifelab.se/researcher/0aad9ec706674ed6ab358a445ba1989d.json"}}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}], "type": "comparative study", "published": "2020-03-06", "journal": {"title": "Science", "issn": "1095-9203", "volume": "367", "issue": "6482", "pages": "eaay5947", "issn-l": "0036-8075"}, "abstract": "The brain, with its diverse physiology and intricate cellular organization, is the most complex organ of the mammalian body. To expand our basic understanding of the neurobiology of the brain and its diseases, we performed a comprehensive molecular dissection of 10 major brain regions and multiple subregions using a variety of transcriptomics methods and antibody-based mapping. This analysis was carried out in the human, pig, and mouse brain to allow the identification of regional expression profiles, as well as to study similarities and differences in expression levels between the three species. The resulting data have been made available in an open-access Brain Atlas resource, part of the Human Protein Atlas, to allow exploration and comparison of the expression of individual protein-coding genes in various parts of the mammalian brain.", "doi": "10.1126/science.aay5947", "pmid": "32139519", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "367/6482/eaay5947"}], "notes": [], "created": "2020-12-07T16:26:57.513Z", "modified": "2024-01-16T13:48:42.811Z"}, {"entity": "publication", "iuid": "da6ca856685141ae9efbd6bfc317bff0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da6ca856685141ae9efbd6bfc317bff0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da6ca856685141ae9efbd6bfc317bff0"}}, "title": "A genome-wide transcriptomic analysis of protein-coding genes in human blood cells.", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Karlsson", "given": "Max J", "initials": "MJ", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Tebani", "given": "Abdellah", "initials": "A", "orcid": "0000-0002-8901-2678", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf47745ed3454f3c819cf6414f140ff0.json"}}, {"family": "Pou", "given": "Christian", "initials": "C", "orcid": "0000-0003-3932-788X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6015314c4c04ee08d7e4358cfb55b9f.json"}}, {"family": "Mikes", "given": "Jaromir", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-5248-8568", "researcher": {"href": "https://publications.scilifelab.se/researcher/d23dc2e614784017b08cb2d8f6b60ded.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a007c2aea2c40ada113ffe87fc3daf0.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-8800-8469", "researcher": {"href": "https://publications.scilifelab.se/researcher/9046f902d0624af0969c4409351f22ba.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal article", "published": "2019-12-20", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "366", "issue": "6472", "pages": null}, "abstract": "Blood is the predominant source for molecular analyses in humans, both in clinical and research settings. It is the target for many therapeutic strategies, emphasizing the need for comprehensive molecular maps of the cells constituting human blood. In this study, we performed a genome-wide transcriptomic analysis of protein-coding genes in sorted blood immune cell populations to characterize the expression levels of each individual gene across the blood cell types. All data are presented in an interactive, open-access Blood Atlas as part of the Human Protein Atlas and are integrated with expression profiles across all major tissues to provide spatial classification of all protein-coding genes. This allows for a genome-wide exploration of the expression profiles across human immune cell populations and all major human tissues and organs.", "doi": "10.1126/science.aax9198", "pmid": "31857451", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Cellular Immunomonitoring": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "366/6472/eaax9198"}], "notes": [], "created": "2019-12-21T09:40:14.331Z", "modified": "2024-01-16T13:48:43.274Z"}, {"entity": "publication", "iuid": "9a66e1ee51af4d9dacf0840a88138663", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a66e1ee51af4d9dacf0840a88138663.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a66e1ee51af4d9dacf0840a88138663"}}, "title": "A pathology atlas of the human cancer transcriptome.", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S", "orcid": "0000-0002-6428-5936", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb2e42e0ef0247ba9365148ab2c164c0.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G", "orcid": "0000-0001-5232-6094", "researcher": {"href": "https://publications.scilifelab.se/researcher/c76df55999a74ebfaada13e0cc775de8.json"}}, {"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca09f57bdc44e7fa33a472f04859a4d.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Liu", "given": "Zhengtao", "initials": "Z", "orcid": "0000-0001-7803-6044", "researcher": {"href": "https://publications.scilifelab.se/researcher/53a62a58b12f4f4c87ebe4135826c91a.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Mattsson", "given": "Johanna", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Glimelius", "given": "Bengt", "initials": "B", "orcid": "0000-0002-5440-791X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e79e661083f49bf90cbbfc19670f404.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd5ff31463cd4345a1fc8351e797ac7f.json"}}, {"family": "Djureinovic", "given": "Dijana", "initials": "D", "orcid": "0000-0002-1852-5409", "researcher": {"href": "https://publications.scilifelab.se/researcher/17058abc202c4da794e35722c1f234df.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}], "type": "journal article", "published": "2017-08-18", "journal": {"volume": "357", "issn": "1095-9203", "issue": "6352", "title": "Science", "pages": "eaan2507", "issn-l": "0036-8075"}, "abstract": "Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes of 17 major cancer types with respect to clinical outcome. A general pattern emerged: Shorter patient survival was associated with up-regulation of genes involved in cell growth and with down-regulation of genes involved in cellular differentiation. Using genome-scale metabolic models, we show that cancer patients have widespread metabolic heterogeneity, highlighting the need for precise and personalized medicine for cancer treatment. All data are presented in an interactive open-access database (www.proteinatlas.org/pathology) to allow genome-wide exploration of the impact of individual proteins on clinical outcomes.", "doi": "10.1126/science.aan2507", "pmid": "28818916", "labels": {"National Genomics Infrastructure": "Service", "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "357/6352/eaan2507"}], "notes": [], "created": "2017-11-03T16:19:27.334Z", "modified": "2024-01-16T13:48:47.600Z"}, {"entity": "publication", "iuid": "9ffdf7a669174f9b940bb01c93fab8a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ffdf7a669174f9b940bb01c93fab8a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ffdf7a669174f9b940bb01c93fab8a9"}}, "title": "A subcellular map of the human proteome.", "authors": [{"family": "Thul", "given": "Peter J", "initials": "PJ", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1441c2fca5d4946987ec975986fcfa2.json"}}, {"family": "\u00c5kesson", "given": "Lovisa", "initials": "L", "orcid": "0000-0002-2387-3491", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b0ca6c2a8f64be89222a6029885b08c.json"}}, {"family": "Wiking", "given": "Mikaela", "initials": "M", "orcid": "0000-0002-6368-6690", "researcher": {"href": "https://publications.scilifelab.se/researcher/b69baef540a14859a7b4fd966c3b9245.json"}}, {"family": "Mahdessian", "given": "Diana", "initials": "D", "orcid": "0000-0003-0750-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc22f13eb21a4c75a6e7cad7686bcc8a.json"}}, {"family": "Geladaki", "given": "Aikaterini", "initials": "A", "orcid": "0000-0002-0530-4252", "researcher": {"href": "https://publications.scilifelab.se/researcher/28081295132343c5bfc4b1e9bcfb8201.json"}}, {"family": "Ait Blal", "given": "Hammou", "initials": "H"}, {"family": "Alm", "given": "Tove", "initials": "T", "orcid": "0000-0002-2643-8241", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a0b5ee89148475581faf42ea53d61bd.json"}}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Bj\u00f6rk", "given": "Lars", "initials": "L", "orcid": "0000-0002-8116-882X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1092280955d44d1f99258f4f812fb6c7.json"}}, {"family": "Breckels", "given": "Lisa M", "initials": "LM", "orcid": "0000-0001-8918-7171", "researcher": {"href": "https://publications.scilifelab.se/researcher/3efbca65f39d4f7aa8df049a39e0c8a9.json"}}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", 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"0000-0002-6428-5936", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb2e42e0ef0247ba9365148ab2c164c0.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}, {"family": "Mulvey", "given": "Claire M", "initials": "CM", "orcid": "0000-0002-2989-2052", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc08b919bd8a423f8a6df8b880979045.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J", "orcid": "0000-0002-9977-5724", "researcher": {"href": "https://publications.scilifelab.se/researcher/34ad1d3b1313460583a16329a0143a1d.json"}}, {"family": "Schutten", "given": "Rutger", "initials": "R", "orcid": "0000-0001-8787-8868", "researcher": {"href": "https://publications.scilifelab.se/researcher/83314cf7a93543bf9cd6f68f9657e99e.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-8800-8469", "researcher": {"href": "https://publications.scilifelab.se/researcher/9046f902d0624af0969c4409351f22ba.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Sullivan", "given": "Devin P", "initials": "DP", "orcid": "0000-0001-6176-108X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2a96138841741f9acff4a50100c2a25.json"}}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Winsnes", "given": "Casper", "initials": "C", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a64c707c8b54b6bbd31dae6485a1392.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Lilley", "given": "Kathryn S", "initials": "KS"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2017-05-26", "journal": {"volume": "356", "issn": "1095-9203", "issue": "6340", "pages": null, "title": "Science", "issn-l": "0036-8075"}, "abstract": "Resolving the spatial distribution of the human proteome at a subcellular level can greatly increase our understanding of human biology and disease. Here we present a comprehensive image-based map of subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of the proteomes of 13 major organelles. Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. This subcellular map can be used to refine existing protein-protein interaction networks and provides an important resource to deconvolute the highly complex architecture of the human cell.", "doi": "10.1126/science.aal3321", "pmid": "28495876", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Spatial Proteomics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "science.aal3321"}], "notes": [], "created": "2017-10-31T15:27:28.787Z", "modified": "2024-01-16T13:48:47.941Z"}]}