{"entity": "researcher", "timestamp": "2026-08-20T20:25:17.891Z", "family": "Ceyhan", "given": "Atakan Burak", "initials": "AB", "orcid": "0009-0004-7279-7482", "affiliations": ["Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London SE1 9RT, UK."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7b1d40cd1ec4d4aa75f133db6d2ff1a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7b1d40cd1ec4d4aa75f133db6d2ff1a"}}, "publications": [{"entity": "publication", "iuid": "a5c1bc6f1ade4bb9bbe7080fcea6a16b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a5c1bc6f1ade4bb9bbe7080fcea6a16b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a5c1bc6f1ade4bb9bbe7080fcea6a16b"}}, "title": "Unravelling the Complexity of Sarcopenia Through a Systems Biology Approach.", "authors": [{"family": "Ceyhan", "given": "Atakan Burak", "initials": "AB", "orcid": "0009-0004-7279-7482", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7b1d40cd1ec4d4aa75f133db6d2ff1a.json"}}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Temel", "given": "Sehime Gulsun", "initials": "SG", "orcid": "0000-0002-9802-0880", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e08a9741204744e78b62958e0bf94794.json"}}, {"family": "Turkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf2f1748757d45cabfe56fdfaccead6a.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "journal article", "published": "2025-09-02", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "26", "issue": "17", "issn-l": null}, "abstract": "Sarcopenia, a significant loss of muscle mass and strength, is an important healthcare problem in the geriatric population. While age-related muscle decline represents the most common form, sarcopenia may also develop as a secondary condition associated with chronic diseases, including cancer, diabetes, chronic obstructive pulmonary disease, and autoimmune disorders. It increases frailty, disability, and fall risk among the elderly while also raising hospitalization rates and associated healthcare costs. Although no pharmaceutical agents have been specifically approved for the treatment of sarcopenia to date, elucidating its underlying molecular mechanisms of sarcopenia through systems biology approaches is essential for the development of novel therapeutic strategies and preventive interventions. This review examines the current definitions of sarcopenia, recent advancements in its management, and the emerging role of systems biology in uncovering potential biomarkers and therapeutic targets. We discuss how these approaches may contribute to the development of novel interventions aimed at enhancing muscle health and improving the quality of life in older adults and provide a summary of the current progress achieved through systems biology methodologies in sarcopenia research.", "doi": "10.3390/ijms26178527", "pmid": "40943447", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12428996"}, {"db": "pii", "key": "ijms26178527"}], "notes": [], "created": "2026-08-20T13:42:00.420Z", "modified": "2026-08-20T13:42:00.527Z"}, {"entity": "publication", "iuid": "35ef6915c3e84674815a2bc5d9f9e404", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/35ef6915c3e84674815a2bc5d9f9e404.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/35ef6915c3e84674815a2bc5d9f9e404"}}, "title": "Identifying Hub Genes and Metabolic Pathways in Collagen VI-Related Dystrophies: A Roadmap to Therapeutic Intervention.", "authors": [{"family": "Ceyhan", "given": "Atakan Burak", "initials": "AB", "orcid": "0009-0004-7279-7482", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7b1d40cd1ec4d4aa75f133db6d2ff1a.json"}}, {"family": "Kaynar", "given": "Ali", "initials": "A", "orcid": "0000-0002-8507-744X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/afaea854b1ad44ec8c6efc6323f516cd.json"}}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Temel", "given": "Sehime Gulsun", "initials": "SG", "orcid": "0000-0002-9802-0880", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e08a9741204744e78b62958e0bf94794.json"}}, {"family": "Turkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf2f1748757d45cabfe56fdfaccead6a.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "journal article", "published": "2024-10-29", "journal": {"title": "Biomolecules", "issn": "2218-273X", "volume": "14", "issue": "11", "issn-l": null}, "abstract": "Collagen VI-related dystrophies (COL6RD) are a group of rare muscle disorders caused by mutations in specific genes responsible for type VI collagen production. It affects muscles, joints, and connective tissues, leading to weakness, joint problems, and structural issues. Currently, there is no effective treatment for COL6RD; its management typically addresses symptoms and complications. Therefore, it is essential to decipher the disease's molecular mechanisms, identify drug targets, and develop effective treatment strategies to treat COL6RD. In this study, we employed differential gene expression analysis, weighted gene co-expression network analysis, and genome-scale metabolic modeling to investigate gene expression patterns in COL6RD patients, uncovering key genes, significant metabolites, and disease-related pathophysiological pathways. First, we performed differential gene expression and weighted gene co-expression network analyses, which led to the identification of 12 genes (CHCHD10, MRPS24, TRIP10, RNF123, MRPS15, NDUFB4, COX10, FUNDC2, MDH2, RPL3L, NDUFB11, PARVB) as potential hub genes involved in the disease. Second, we utilized a drug repurposing strategy to identify pharmaceutical candidates that could potentially modulate these genes and be effective in the treatment. Next, we utilized context-specific genome-scale metabolic models to compare metabolic variations between healthy individuals and COL6RD patients. Finally, we conducted reporter metabolite analysis to identify reporter metabolites (e.g., phosphatidates, nicotinate ribonucleotide, ubiquinol, ferricytochrome C). In summary, our analysis revealed critical genes and pathways associated with COL6RD and identified potential targets, reporter metabolites, and candidate drugs for therapeutic interventions.", "doi": "10.3390/biom14111376", "pmid": "39595553", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11592009"}, {"db": "pii", "key": "biom14111376"}, {"db": "GEO", "key": "GSE103608"}], "notes": [], "created": "2026-08-20T13:38:48.538Z", "modified": "2026-08-20T13:38:48.796Z"}, {"entity": "publication", "iuid": "01c3e943e14c4367bb8fd9cc7c8d2bba", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/01c3e943e14c4367bb8fd9cc7c8d2bba.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/01c3e943e14c4367bb8fd9cc7c8d2bba"}}, "title": "Unveiling the Molecular Mechanisms of Glioblastoma through an Integrated Network-Based Approach.", "authors": [{"family": "Kaynar", "given": "Ali", "initials": "A", "orcid": "0000-0002-8507-744X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/afaea854b1ad44ec8c6efc6323f516cd.json"}}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Ceyhan", "given": "Atakan Burak", "initials": "AB", "orcid": "0009-0004-7279-7482", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7b1d40cd1ec4d4aa75f133db6d2ff1a.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Turkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf2f1748757d45cabfe56fdfaccead6a.json"}}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}], "type": "journal article", "published": "2024-10-01", "journal": {"title": "Biomedicines", "issn": "2227-9059", "volume": "12", "issue": "10", "issn-l": null}, "abstract": "Background/Objectives: Despite current treatments extending the lifespan of Glioblastoma (GBM) patients, the average survival time is around 15-18 months, underscoring the fatality of GBM. This study aims to investigate the impact of sample heterogeneity on gene expression in GBM, identify key metabolic pathways and gene modules, and explore potential therapeutic targets. Methods: In this study, we analysed GBM transcriptome data derived from The Cancer Genome Atlas (TCGA) using genome-scale metabolic models (GEMs) and co-expression networks. We examine transcriptome data incorporating tumour purity scores (TPSs), allowing us to assess the impact of sample heterogeneity on gene expression profiles. We analysed the metabolic profile of GBM by generating condition-specific GEMs based on the TPS group. Results: Our findings revealed that over 90% of genes showing brain and glioma specificity in RNA expression demonstrate a high positive correlation, underscoring their expression is dominated by glioma cells. Conversely, negatively correlated genes are strongly associated with immune responses, indicating a complex interaction between glioma and immune pathways and non-tumorigenic cell dominance on gene expression. TPS-based metabolic profile analysis was supported by reporter metabolite analysis, highlighting several metabolic pathways, including arachidonic acid, kynurenine and NAD pathway. Through co-expression network analysis, we identified modules that significantly overlap with TPS-correlated genes. Notably, SOX11 and GSX1 are upregulated in High TPS, show a high correlation with TPS, and emerged as promising therapeutic targets. Additionally, NCAM1 exhibits a high centrality score within the co-expression module, which shows a positive correlation with TPS. Moreover, LILRB4, an immune-related gene expressed in the brain, showed a negative correlation and upregulated in Low TPS, highlighting the importance of modulating immune responses in the GBM mechanism. Conclusions: Our study uncovers sample heterogeneity's impact on gene expression and the molecular mechanisms driving GBM, and it identifies potential therapeutic targets for developing effective treatments for GBM patients.", "doi": "10.3390/biomedicines12102237", "pmid": "39457550", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11504402"}, {"db": "pii", "key": "biomedicines12102237"}], "notes": [], "created": "2026-08-20T13:38:56.812Z", "modified": "2026-08-20T13:38:56.909Z"}]}