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Publications

50 latest publications

[1]
Dahl, L., Bendes, A., Bueno Alvez, M., Albrecht, V., Aghelpasand, H., Björkander, S. ... Schwenk, J. M. (2026). Exploration of immune phenotypes in self-sampling citizens. iScience, 29(2).
[2]
Shi, Z., Ren, H., Lin, C., Li, F., Wu, M., Yang, F. ... Zhong, H. (2026). Tissue-resident microbiota impacts colorectal cancer progression and prognosis. Nature Communications, 17(1).
[3]
Bertilsson, F., Hikmet, F., Hansen, J. N., Uhlén, M., Méar, L. & Lindskog, C. (2026). A High-Resolution Subcellular Map of Proteins in Cells with Motile Cilia. Journal of Proteome Research, 25(1), 231-243.
[4]
Jin, S., Cenier, A., Wetzel, D., Arefaine, B., Moreno-Gonzalez, M., Stamouli, M. ... Schirmer, M. (2026). Microbial collagenase activity is linked to oral–gut translocation in advanced chronic liver disease. Nature Microbiology, 11(1), 211-227.
[5]
Chakaroun, R. M., Pradhan, M., Björnson, E., Arvidsson, D., Fridolfsson, J., Gummesson, A. ... Bäckhed, F. (2026). Multi-omic definition of metabolic obesity through adipose tissue–microbiome interactions. Nature Medicine, 32(1), 113-125.
[6]
Zhu, W., Fung, K., Dhami, P., Sharpe, P., Krivanek, J., Nibali, L. ... Neves, V. C.M. (2026). Characterising the Periodontal Granulation Tissue Using scRNAseq. Journal of Clinical Periodontology, 53(2), 308-320.
[7]
Lundgren, P., Pivodic, A., Nilsson, A. K., Hellgren, G., Danielsson, H., Wackernagel, D. ... Hellström, A. (2025). Platelet characteristics in extremely preterm infants after fatty acid supplementation : a randomized controlled trial. Pediatric Research, 98(2), 680-689.
[8]
Vurgun, E., Tepgec, F., Yuruyen, M., Yilmaz, O., Mardinoglu, A., Uyguner, Z. O. & Gedikbasi, A. (2025). Metabolomics-based potential plasma metabolite biomarkers for metabolic syndrome and its five components : a casecontrol study. FEBS Open Bio, 15, 402-402.
[9]
Tepgec, F., Yuruyen, M., Yilmaz, O., Vurgun, E., Mardinoglu, A., Gedikbasi, A. & Uyguner, Z. O. (2025). Genomic-transcriptomic differences in peripheral blood of healthy aging : insights for neurodegenerative disease. FEBS Open Bio, 15, 51-51.
[10]
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.
[11]
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).
[12]
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).
[13]
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.
[14]
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).
[15]
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.
[16]
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.
[17]
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.
[18]
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.
[19]
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.
[20]
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).
[21]
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).
[22]
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.
[23]
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, 188(24), 6804-6824.e16.
[24]
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).
[25]
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, 58(8), 2120-2136.e5.
[26]
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).
[27]
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.
[28]
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).
[29]
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.
[30]
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).
[31]
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).
[32]
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).
[33]
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).
[34]
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.
[35]
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).
[36]
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).
[37]
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.
[38]
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).
[39]
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).
[40]
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).
[41]
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).
[42]
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).
[43]
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).
[44]
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.
[45]
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.
[46]
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).
[47]
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).
[48]
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.
[49]
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).
[50]
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.