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Publications

50 latest publications

[1]
Shi, Z., Zhu, T., Ren, H., Li, F., Wu, M., Yang, F. ... Zhong, H. (2025). Distribution and prognostic impacts of enterobacteriaceae-derived virulence factor genes in colorectal cancer. Gut, 74(SUPPL_3), A183-A186.
[2]
Jönsson, M., Möller, M., Schierholz, L., Dorka, N., Tegel, H., Lundberg, E. ... Hober, S. (2025). Engineered calcium-regulated affinity protein for efficient internalization and lysosomal toxin delivery. Proceedings of the National Academy of Sciences of the United States of America, 122(48).
[3]
Cankaya, S., Safa, S. S., Karakus, A., Savcili, M., Hanoglu, L., Mardinoglu, A. ... Yulug, B. (2025). Depression is an independent risk factor for stroke reccurence and cognitive impairment in stroke patients. Translational Psychiatry, 15(1).
[4]
Cankaya, S., Akturk, A., Karakus, A., Hanoğlu, L., Mardinoglu, A. & Yulug, B. (2025). Targeting the parietal memory network with tDCS in MCI : study protocol for a randomized controlled trial. Frontiers in Human Neuroscience, 19.
[5]
Tan, Z., Zhong, W., Danielsson, H., Arzoomand, A., Lakshmikanth, T., Chen, Q. ... Brodin, P. (2025). Immune development differs between preterm newborns fed mothers' own milk and donor milk. iScience, 28(7).
[6]
Keiser, L. S., Gatenil, P. P., Zhu, Y., Deng, K., Waldburger, L., Gin, J. W. ... Keasling, J. D. (2025). Engineering Polyketide Stereocenters with Ketoreductase Domain Exchanges. Journal of the American Chemical Society, 147(46), 42237-42252.
[7]
Mardinoglu, A., Turkez, H., Shong, M., Srinivasulu, V. P., Nielsen, J., Palsson, B. O. ... Uhlén, M. (2025). Longitudinal big biological data in the AI era. Molecular Systems Biology, 21(9), 1147-1165.
[8]
Cengic, I. & Hudson, E. P. (2025). Establishing a Malonyl-CoA Biosensor for the Two Model Cyanobacteria Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942. ACS Synthetic Biology, 14(7), 2865-2877.
[9]
Hoffmann, U. A., Schuppe, A. Z., Knave, A., Sporre, E., Brismar, H., Englund, E. ... Hudson, E. P. (2025). A Cyanobacterial Screening Platform for Rubisco Mutant Variants. ACS Synthetic Biology, 14(7), 2619-2633.
[10]
Zhu, W., Fung, K., Dhami, P., Sharpe, P., Krivanek, J., Nibali, L. ... Neves, V. C.M. (2025). Characterising the Periodontal Granulation Tissue Using scRNAseq. Journal of Clinical Periodontology.
[11]
Babanezhad Harikandei, K., Salehi, P., Hasanpour, Z., Bararjanian, M., Kim, W., Asghari, S. M. & Mardinoglu, A. (2025). Noscapine-bile acid hybrids as novel anticancer agents. RSC Medicinal Chemistry, 16(11), 5511-5533.
[12]
Yulug, B., Uygur, B., Sayman, D., Cankaya, S., Ayyıldız, B., Ayyıldız, S. ... Mardinoglu, A. (2025). The Role of Willpower in Major Depressive Disorder: An fMRI Study. Brain and Behavior, 15(10).
[13]
Masson, H. O., Di Giusto, P., Kuo, C. C., Malm, M., Lundqvist, M., Sivertsson, Å. ... Lewis, N. E. (2025). Deciphering the determinants of recombinant protein expression across the human secretome. Proceedings of the National Academy of Sciences of the United States of America, 122(41).
[14]
Li, M., Kim, W., Jin, H., Yang, H., Kong, X., Song, X. ... Mardinoglu, A. (2025). Anticancer effects and mechanisms of Pulsatilla chinensis, Bupleurum chinense and Polyporus umbellatus on human lung carcinoma and hepatoma cells. Computational and Structural Biotechnology Journal, 27, 3066-3078.
[15]
Hansen, J. N., Sun, H., Kahnert, K., Westenius, E., Johannesson, A., Villegas, C. ... Käller Lundberg, E. (2025). Intrinsic heterogeneity of primary cilia revealed through spatial proteomics. Cell.
[16]
Ceyhan, A. B., Altay, Ö., Zhang, C., Temel, S. G., Turkez, H. & Mardinoglu, A. (2025). Unravelling the Complexity of Sarcopenia Through a Systems Biology Approach. International Journal of Molecular Sciences, 26(17).
[17]
Lautenbach, M. J., Wyss, K., Yman, V., Foroogh, F., Satarvandi, D., Mousavian, Z. ... Färnert, A. (2025). Systems analysis of clinical malaria reveals proteomic perturbation and innate-adaptive crosstalk linked to disease severity. Immunity.
[18]
Song, X., Jin, H., Li, X., Yuan, M., Yang, H., Sato, Y. ... Mardinoglu, A. (2025). Systematically identification of survival-associated eQTLs in a Japanese kidney cancer cohort. PLOS Genetics, 21(7 July).
[19]
Dahlsson Leitao, C., Löfblom, J., Nygren, P.-Å., Hober, S., Uhlén, M. & Ståhl, S. (2025). The many virtues of staphylococcal protein A : A journey from N to C terminus. Journal of Biotechnology, 406, 272-280.
[20]
Wang, J., Zenere, A., Wang, X., Bergström, G., Edfors, F., Uhlén, M. & Zhong, W. (2025). Longitudinal analysis of genetic and environmental interplay in human metabolic profiles and the implication for metabolic health. Genome Medicine, 17(1).
[21]
Johansson, E., Iglesias, M. J., Odeberg, J. & Edfors, F. (2025). Shaping the future of precision medicine: plasma proteomics to uncover insights in thrombosis. Expert Review of Proteomics, 22(6), 237-254.
[22]
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).
[23]
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).
[24]
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).
[25]
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).
[26]
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.
[27]
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).
[28]
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).
[29]
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.
[30]
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).
[31]
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).
[32]
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).
[33]
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).
[34]
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).
[35]
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).
[36]
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.
[37]
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.
[38]
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).
[39]
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).
[40]
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.
[41]
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).
[42]
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.
[43]
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.
[44]
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.
[45]
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.
[46]
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.
[47]
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).
[48]
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).
[49]
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).
[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.