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Publications

50 latest publications

[1]
Shi, M., Shi, M., Karlsson, M., Alvez, M. B., Jin, H., Yuan, M. ... et al., (2025). A resource for whole-body gene expression map of human tissues based on integration of single cell and bulk transcriptomics. Genome Biology, 26(1).
[2]
Johansson, C., Schrama, E. J., Kotol, D., Hober, A., Koeks, Z., van de Velde, N. M. ... Al-Khalili Szigyarto, C. (2025). Contrasting Becker and Duchenne muscular dystrophy serum biomarker candidates by using data independent acquisition LC-MS/MS. Skeletal Muscle, 15(1).
[3]
Clasen, F., Yildirim, S., Arıkan, M., Garcia-Guevara, F., Hanoğlu, L., Yılmaz, N. H. ... Shoaie, S. (2025). Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson’s disease and cognitive decline pathophysiology. Gut microbes, 17(1).
[4]
Presacan, O., Dorobantiu, A., Isaksen, J. L., Willi, T., Graff, C., Riegler, M. A. ... Thambawita, V. (2025). Evaluating the feasibility of 12-lead electrocardiogram reconstruction from limited leads using deep learning. Communications Medicine, 5(1).
[5]
Bergentall, M., Tremaroli, V., Sun, C., Henricsson, M., Khan, M. T., Mannerås Holm, L. ... Bäckhed, F. (2025). Gut microbiota mediates SREBP-1c-driven hepatic lipogenesis and steatosis in response to zero-fat high-sucrose diet. Molecular Metabolism, 97.
[6]
Baek, J. W., Lim, S., Park, N., Song, B., Kirtipal, N., Nielsen, J. ... Lee, S. (2025). Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions. npj Biofilms and Microbiomes, 11(1).
[7]
Karlsson, A., Sporre, E., Strandberg, L., Tóth, S. Z. & Hudson, E. P. (2025). Assessing Metabolite Interactions With Chloroplastic Proteins via the PISA Assay. Bio-protocol, 15(9).
[8]
Shi, M. (2025). Systems Biology Approaches for Target Identification and Therapeutic Development in Chronic Diseases : Integrating Bulk and Single-Cell Transcriptomics (Doctoral thesis , KTH Royal Institute of Technology, TRITA-CBH-FOU 2025:17). Retrieved from https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-363184.
[9]
Lee, S., Arefaine, B., Begum, N., Stamouli, M., Witherden, E., Mohamad, M. ... Patel, V. C. (2025). Oral-gut microbiome interactions in advanced cirrhosis : characterisation of pathogenic enterotypes and salivatypes, virulence factors and antimicrobial resistance. Journal of Hepatology, 82(4).
[10]
Villanueva Raisman, A., Kotol, D., Altay, Ö., Mardinoglu, A., Atak, D., Yurdaydin, C. ... Edfors, F. (2025). Advancing Chronic Liver Disease Diagnoses: Targeted Proteomics for the Non-Invasive Detection of Fibrosis. Livers, 5(1).
[11]
Mikaeloff, F., Mardinoglu, A. & Neogi, U. (2025). Host Plasma Microenvironment in Immunometabolically Impaired HIV Infection Leads to Dysregulated Monocyte Function and Synaptic Transmission Ex Vivo. Advanced Science, 12(16).
[12]
Turkez, H., Oner, S., Yildirim, O. C., Arslan, M. E., Dimmito, M. P., Kahraman, C. Y. ... Mardinoglu, A. (2025). Synthesis and Characterization of Memantine-Loaded Niosomes for Enhanced Alzheimer's Disease Targeting. Pharmaceutics, 17(2).
[13]
Buhlak, S., Abad, N., Akachar, J., Saffour, S., Kesgun, Y., Dik, S. ... Mardinoglu, A. (2025). Design, Synthesis, and Computational Evaluation of 3,4-Dihydroquinolin-2(1H)-One Analogues as Potential VEGFR2 Inhibitors in Glioblastoma Multiforme. Pharmaceuticals, 18(2).
[14]
Yang, H., Atak, D., Yuan, M., Li, M., Altay, Ö., Demirtas, E. ... Zeybel, M. (2025). Integrative proteo-transcriptomic characterization of advanced fibrosis in chronic liver disease across etiologies. Cell Reports Medicine, 6(2).
[15]
Yang, H., Zhang, C., Kim, W., Shi, M., Kiliclioglu, M., Bayram, C. ... Mardinoglu, A. (2025). Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats. eLIFE, 13.
[16]
Soleimani, S., Albayrak, O., Somay, K., Yang, H., Yigit, B., Ulukan, B. ... Zeybel, M. (2025). Cellular and immune landscape of chronic liver diseases : insights from immunophenotyping. Frontiers in Molecular Biosciences, 11.
[17]
Li, Y., Wang, B., Zheng, Y., Kang, H., He, A., Zhao, L. ... Chen, X. (2025). The multifaceted role of post-translational modifications of LSD1 in cellular processes and disease pathogenesis. Genes and Diseases, 12(3).
[18]
Carrasquer-Alvarez, E., Hoffmann, U. A., Geissler, A. S., Knave, A., Gorodkin, J., Seemann, S. E. ... Frigaard, N.-U. (2025). Photosynthesis in Synechocystis sp. PCC 6803 is not optimally regulated under very high CO2. Applied Microbiology and Biotechnology, 109(1).
[19]
Sebhaoui, J., Ashraf, S., Iqbal, S., Hajji, M., Belmen, B., Yesilyurt, G. ... Mardinoglu, A. (2025). Synthesis of novel tetrahydrobenzo[b]thiophene-3-carbonitrile (THBTC)-based heterocycles : Structural insights, reactivity profiles, and in-silico bioactivity studies. Journal of Molecular Structure, 1326.
[20]
Yulug, B., Altay, Ö., Lei, X., Hanoglu, L., Cankaya, S., Velioglu, H. A. ... Mardinoglu, A. (2025). Multi-omics characterization of improved cognitive functions in Parkinson’s disease patients after the combined metabolic activator treatment : a randomized, double-blinded, placebo-controlled phase II trial. Brain Communications, 7(1).
[21]
El Hafi, M., Bouzian, Y., Parvizi, N., Kim, W., Subaşioğlu, M., Ozcan, M. ... Mardinoglu, A. (2025). Synthesis and biological assessment of BUB1B inhibitors for the treatment of clear cell renal cell carcinoma. European Journal of Medicinal Chemistry, 285.
[22]
Koçak, G., Uyulgan, S., Polatlı, E., Sarı, V., Kahveci, B., Bursali, A. ... Güven, S. (2024). Generation of Anterior Segment of the Eye Cells from hiPSCs in Microfluidic Platforms. Advanced Biology, 8(5).
[23]
Tóth, D., Tengölics, R., Aarabi, F., Karlsson, A., Vidal-Meireles, A., Kovács, L. ... Tóth, S. Z. (2024). Chloroplastic ascorbate modifies plant metabolism and may act as a metabolite signal regardless of oxidative stress. Plant Physiology, 196(2), 1691-1711.
[24]
Wang, B., Wang, S. W., Zhou, Y., Wang, S. P., Gao, Y., Liu, H. M. ... Dai, X. J. (2024). Discovery of 2-Aryl-4-aminoquinazolin-Based LSD1 Inhibitors to Activate Immune Response in Gastric Cancer. Journal of Medicinal Chemistry, 67(18), 16165-16184.
[25]
Zheng, T., Kotol, D., Sjöberg, R., Mitsios, N., Uhlén, M., Zhong, W. ... Mulder, J. (2024). Characterization of reduced astrocyte creatine kinase levels in Alzheimer's disease. Glia, 72(9), 1590-1603.
[26]
Turkez, H., Tozlu, O. O., Arslan, M. E., Baba, C., Saracoglu, M. M., Yıldız, E. ... Mardinoglu, A. (2024). Boric Acid and Borax Protect Human Lymphocytes from Oxidative Stress and Genotoxicity Induced by 3-Monochloropropane-1,2-diol. Biological Trace Element Research, 202(11), 5006-5016.
[27]
Campagna, A., Clasen, F., Portlock, T. J., Zampini, M., Ficara, F., Crisafulli, L. ... Shoaie, S. (2024). Clinical Relevance of the Integrative Analysis of Gut Microbiome and Metabolomics in Myeloid Neoplasms : Correlations with Genomic Profiles, Treatment Response/Complications and Clinical Outcome. Blood, 144(Supplement 1), 104-104.
[28]
Brouwer, E. M., Medipally, H. K., Schwab, S., Song, S., Nowaczyk, M. M. & Hagemann, M. (2024). Characterization of the oxygen-tolerant formate dehydrogenase from Clostridium carboxidivorans. Frontiers in Microbiology, 15.
[29]
Shabestary, K., Klamt, S., Link, H., Mahadevan, R., Steuer, R. & Hudson, E. P. (2024). Design of microbial catalysts for two-stage processes. Nature Reviews Bioengineering, 2(12), 1039-1055.
[30]
De Vries, S., Degan, C., Tobin, R., Jimenez-Requena, A., Ajeenah, A., Johansson, C. ... Dang, U. (2024). Development of monitoring biomarker signatures in Duchenne muscular dystrophy. Neuromuscular Disorders, 43.
[31]
Chesner, L. N., Polesso, F., Graff, J. N., Hawley, J. E., Smith, A. K., Lundberg, A. ... Moran, A. E. (2024). Androgen receptor inhibition increases MHC Class I expression and improves immune response in prostate cancer. Cancer Discovery, 15(3), 481-494.
[32]
Baudin, J., Hernandez-Baixauli, J., Romero-Giménez, J., Yang, H., Mulero, F., Puiggròs, F. ... Caimari, A. (2024). A cocktail of histidine, carnosine, cysteine and serine reduces adiposity and improves metabolic health and adipose tissue immunometabolic function in ovariectomized rats. Biomedicine and Pharmacotherapy, 179.
[33]
Lee, S., Portlock, T. J., Garcia-Guevara, J. F., von Feilitzen, K., Johansson, F., Zhang, C. ... Shoaie, S. (2024). Global compositional and functional states of the human gut microbiome in health and disease. Genome Research, 34(6), 967-978.
[34]
Kaynar, A., Ozcan, M., Li, X., Turkez, H., Zhang, C., Uhlén, M. ... Mardinoglu, A. (2024). Discovery of a Therapeutic Agent for Glioblastoma Using a Systems Biology-Based Drug Repositioning Approach. International Journal of Molecular Sciences, 25(14).
[35]
Iqbal, S., Islam, M. Z., Ashraf, S., Kim, W., AL-Sharabi, A. A., Ozcan, M. ... Mardinoglu, A. (2024). Discovery of Cell-Permeable Allosteric Inhibitors of Liver Pyruvate Kinase: Design and Synthesis of Sulfone-Based Urolithins. International Journal of Molecular Sciences, 25(14).
[36]
Bouzian, Y., El Hafi, M., Parvizi, N., Kim, W., Subaşioğlu, M., Ozcan, M. ... Mardinoglu, A. (2024). Design and evaluation of novel inhibitors for the treatment of clear cell renal cell carcinoma. Bioorganic chemistry, 151.
[37]
Snanoudj, S., Derambure, C., Zhang, C., Hai Yen, N. T., Lesueur, C., Coutant, S. ... Tebani, A. (2024). Genome-wide expression analysis in a Fabry disease human podocyte cell line. Heliyon, 10(14).
[38]
Jin, H., Zhang, C., Nagenborg, J., Juhasz, P., Ruder, A. V., Sikkink, C. J.J.M. ... Biessen, E. A.L. (2024). Genome-scale metabolic network of human carotid plaque reveals the pivotal role of glutamine/glutamate metabolism in macrophage modulating plaque inflammation and vulnerability. Cardiovascular Diabetology, 23(1).
[39]
Han, X., Sandalova, T., Zhang, C., Mardinoglu, A., Achour, A. & Sun, R. (2024). High Resolution Crystal Structure of the Pyruvate Kinase Tetramer in Complex with the Allosteric Activator Mitapivat/AG-348. Crystals, 14(5).
[40]
Dannemeyer, M., Berling, A., Kanje, S., Enstedt, H., Xu, L., Afshari, D. ... Tegel, H. (2024). Fast and robust recombinant protein production utilizing episomal stable pools in WAVE bioreactors. Protein Expression and Purification, 221.
[41]
Iqbal, S., Sebhaoui, J., Ashraf, S., Özcan, M., Kim, W., Belmen, B. ... Mardinoglu, A. (2024). Design and synthesis of novel JNK inhibitors targeting liver pyruvate kinase for the treatment of non-alcoholic fatty liver disease and hepatocellular carcinoma. Bioorganic chemistry, 147.
[42]
Altay, Ö., Yang, H., Yildirim, S., Bayram, C., Bolat, I., Oner, S. ... Mardinoglu, A. (2024). Combined Metabolic Activators with Different NAD+ Precursors Improve Metabolic Functions in the Animal Models of Neurodegenerative Diseases. Biomedicines, 12(4).
[43]
Mohammadi, E., Dashti, S., Shafizade, N., Jin, H., Zhang, C., Lam, S. ... Sekhavati, M. H. (2024). Drug repositioning for immunotherapy in breast cancer using single-cell analysis. npj Systems Biology and Applications, 10(1).
[44]
Klevebro, S., Kebede Merid, S., Sjöbom, U., Zhong, W., Danielsson, H., Wackernagel, D. ... Nilsson, A. K. (2024). Arachidonic acid and docosahexaenoic acid levels correlate with the inflammation proteome in extremely preterm infants. Clinical Nutrition, 43(5), 1162-1170.
[45]
Bonanini, F., Singh, M., Yang, H., Kurek, D., Harms, A. C., Mardinoglu, A. & Hankemeier, T. (2024). A comparison between different human hepatocyte models reveals profound differences in net glucose production, lipid composition and metabolism in vitro. Experimental Cell Research, 437(1).
[46]
Charras, Q., Rey, P., Guillemain, D., Dourguin, F., Laganier, H., Peschoux, S. ... Jungas, C. (2024). An efficient protocol for extracting thylakoid membranes and total leaf proteins from Posidonia oceanica and other polyphenol-rich plants. Plant Methods, 20(1).
[47]
Lu, C., Donners, M. M.P.C., de Baaij, J. B.J., Jin, H., Otten, J. J.T., Manca, M. ... Biessen, E. A.L. (2024). Identification of a gene network driving the attenuated response to lipopolysaccharide of monocytes from hypertensive coronary artery disease patients. Frontiers in Immunology, 15.
[48]
Öling, S., Struck, E., Noreen-Thorsen, M., Zwahlen, M., von Feilitzen, K., Odeberg, J. ... Butler, L. M. (2024). A human stomach cell type transcriptome atlas. BMC Biology, 22(1).
[49]
Turkez, H., Arslan, M. E., Selvitopi, H., Kadi, A., Oner, S. & Mardinoglu, A. (2024). Drug Synergism of Anticancer Action in Combination with Favipiravir and Paclitaxel on Neuroblastoma Cells. Medicina, 60(1).
[50]
Gouleni, N., Di Rienzo, A., Oner, S., Karagoz, C., Arslan, M. E., Mardinoglu, A. ... Cacciatore, I. (2024). Anticancer Potential of Novel Cinnamoyl Derivatives against U87MG and SHSY-5Y Cell Lines. Anti-Cancer Agents in Medicinal Chemistry, 24(1), 39-49.