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Staff Profile

Najib Naamane

Bioinformatician

  • Address: 3rd Floor, William Leech Building, M3.127
    Translational and Clinical Research Institute
    Musculoskeletal Research Group
    The Medical School, Newcastle University
    Newcastle upon Tyne NE2 4HH
Publications

  • Articles

    • Brown PM, Anderson AE, Naamane N, Lendrem DW, Morgan AW, Isaacs JD, Pratt AG. Adenosine metabolic signature in circulating CD4+ T cells predicts remission in rheumatoid arthritis. RMD Open 2024, 10(1), e003858.
    • Vaskimo LM, Gomon G, Naamane N, Cordell HJ, Pratt A, Knevel R. The Application of Genetic Risk Scores in Rheumatic Diseases: A Perspective. Genes 2023, 14(12), 2167.
    • Cooles FAH, Tarn J, Lendrem DW, Naamane N, Lin CMA, Millar B, Maney NJ, Anderson AE, Thalayasingam N, Diboll J, Bondet V, Duffy D, Barnes MR, Smith GR, Ng S, Watson D, Henkin R, Cope AP, Reynard LN, Pratt AG, Isaacs JD. Interferon-α-mediated therapeutic resistance in early rheumatoid arthritis implicates epigenetic reprogramming. Annals of the Rheumatic Diseases 2022, 81(9), 1214-1223.
    • Vidal-Pedrola G, Naamane N, Cameron JA, Pratt AG, Mellor AL, Isaacs JD, Scheel-Toellner D, Anderson AE. Characterization of age-associated B cells in early drug-naïve rheumatoid arthritis patients. Immunology 2022, epub ahead of print.
    • Howey R, Clark AD, Naamane N, Reynard LN, Pratt AG, Cordell HJ. A Bayesian network approach incorporating imputation of missing data enables exploratory analysis of complex causal biological relationships. PLOS Genetics 2021, 17(9), e1009811.
    • Clark AD, Nair N, Anderson AE, Thalayasingam N, Naamane N, Skelton AJ, Diboll J, Barton A, Eyre S, Isaacs JD, Pratt AG, Reynard LN. Lymphocyte DNA methylation mediates genetic risk at shared immune-mediated disease loci. Journal of Allergy and Clinical Immunology 2020, 145(5), 1438-1451.
    • Ridgley LA, Anderson AE, Maney NJ, Naamane N, Skelton AJ, Lawson CA, Emery P, Isaacs JD, Carmody RJ, Pratt AG. IL-6 Mediated Transcriptional Programming of Naïve CD4+ T Cells in Early Rheumatoid Arthritis Drives Dysregulated Effector Function. Frontiers in Immunology 2019, 10, 1535.
    • Lendrem BC, Lendrem DW, Pratt AG, Naamane N, McMeekin P, Ng W-F, Allen AJ, Power M, Isaacs JD. Between a ROC and a hard place: Teaching prevalence plots to understand real world biomarker performance in the clinic. Pharmaceutical Statistics 2019, 18(6), 632-635.
    • Cunha DA, Gurzov EN, Naamane N, Ortis F, Cardozo AK, Bugliani M, Marchetti P, Eizirik DL, Cnop M. JunB protects β-cells from lipotoxicity via the XBP1-AKT pathway. Cell Death & Differentiation 2014, 21(8), 1313-24.
    • Wolden-Kirk H, Overbergh L, Gysemans C, Brusgaard K, Naamane N, VanLommel L, Schuit F, Eizirik DL, Christesen H, Mathieu C. Unraveling the effects of 1,25(OH)2D3 on global gene expression in pancreatic islets. Journal of Steroid Biochemistry and Molecular Biology 2013, 136, 68-79.
    • Gurzov EN, Barthson J, Marhfour I, Ortis F, Naamane N, Igoillo-Esteve M, Gysemans C, Mathieu C, Kitajima S, Marchetti P, Ørntoft TF, Bakiri L, Wagner EF, Eizirik DL. Pancreatic β-cells activate a JunB/ATF3-dependent survival pathway during inflammation. Oncogene 2012, 31(13), 1723-32.
    • Volkmar M, Dedeurwaerder S, Cunha DA, Ndlovu MN, Defrance M, Deplus R, Calonne E, Volkmar U, Igoillo-Esteve M, Naamane N, Del-Guerra S, Masini M, Bugliani M, Marchetti P, Cnop M, Eizirik DL, Fuks F. DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients. EMBO J 2012, 31(6), 1405-26.
    • Cunha DA, Igoillo-Esteve M, Gurzov EN, Germano CM, Naamane N, Marhfour I, Fukaya M, Vanderwinden JM, Gysemans C, Mathieu C, Marselli L, Marchetti P, Harding HP, Ron D, Eizirik DL, Cnop M. Death protein 5 and p53-upregulated modulator of apoptosis mediate the endoplasmic reticulum stress-mitochondrial dialog triggering lipotoxic rodent and human beta-cell apoptosis. Diabetes 2012, 61(11), 2763-75.
    • Moore F, Naamane N, Colli ML, Bouckenooghe T, Ortis F, Gurzov EN, Igoillo-Esteve M, Mathieu C, Bontempi G, Thykjaer T, Ørntoft TF, Eizirik DL. STAT1 is a master regulator of pancreatic {beta}-cell apoptosis and islet inflammation. J Biol Chem 2011, 286(2), 929-41.
    • Liechti R, Csárdi G, Bergmann S, Schütz F, Sengstag T, Boj SF, Servitja JM, Ferrer J, Van-Lommel L, Schuit F, Klinger S, Thorens B, Naamane N, Eizirik DL, Marselli L, Bugliani M, Marchetti P, Lucas S, Holm C, Jongeneel CV, Xenarios I. EuroDia: a beta-cell gene expression resource. Database 2010, 2010, baq024.
    • Ortis F, Naamane N, Flamez D, Ladrière L, Moore F, Cunha DA, Colli ML, Thykjaer T, Thorsen K, Orntoft TF, Eizirik DL. Cytokines interleukin-1beta and tumor necrosis factor-alpha regulate different transcriptional and alternative splicing networks in primary beta-cells. Diabetes 2010, 59(2), 358-74.
    • Ortis F, Pirot P, Naamane N, Kreins AY, Rasschaert J, Moore F, Théâtre E, Verhaeghe C, Magnusson NE, Chariot A, Orntoft TF, Eizirik DL. Induction of nuclear factor-kappaB and its downstream genes by TNF-alpha and IL-1beta has a pro-apoptotic role in pancreatic beta cells. Diabetologia 2008, 51(7), 1213-25.
    • Naamane N, Helden JV, Eizirik DL. In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells. BMC bioinformatics 2007, 8, 55.
    • Pirot P, Naamane N, Libert F, Magnusson NE, Ørntoft TF, Cardozo AK, Eizirik DL. Global profiling of genes modified by endoplasmic reticulum stress in pancreatic beta cells reveals the early degradation of insulin mRNAs. Diabetologia 2007, 50(5), 1006-14.

  • Review

    • Kutlu B, Naamane N, Berthou L, Eizirik DL. New approaches for in silico identification of cytokine-modified beta cell gene networks. Annals of the New York Academy of Sciences 2004, 1037, 41-58.