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Publications

50 latest publications

[1]
Akbas, E., Othman, K. A., Çelikezen, F. Ç., Aydogan Ejder, N., Turkez, H., Yapca, O. E. & Mardinoglu, A. (2024). Synthesis and Biological Evaluation of Novel Benzylidene Thiazolo Pyrimidin-3(5H)-One Derivatives. Polycyclic aromatic compounds (Print), 44(5), 3061-3078.
[2]
Ceyhan, A. B., Ozcan, M., Kim, W., Li, X., Altay, Ö., Zhang, C. & Mardinoglu, A. (2024). Novel drug targets and molecular mechanisms for sarcopenia based on systems biology. Biomedicine and Pharmacotherapy, 176.
[3]
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).
[4]
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.
[5]
Yang, H. (2024). Integrated understanding and targeting metabolic dysregulation in chronic liver disease : A multi-omics and systems biology perspective (Doctoral thesis , KTH Royal Institute of Technology, Stockholm, TRITA-CBH-FOU 2024:25). Retrieved from https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-346481.
[6]
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.
[7]
Ashraf, S., Iqbal, S., Sebhaoui, J., Özcan, M., Kim, W., Belmen, B. ... Mardinoglu, A. (2024). Synthesis, spectroscopic characterization, DFT and molecular docking of N-(3-cyano-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl) naphthalene-1-sulfonamide derivatives. Journal of Molecular Structure, 1312.
[8]
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).
[9]
Yang, H., Zhang, C., Kim, W., Shi, M., Kiliclioglu, M., Bayram, C., Bolat, I., Tozlu, Ö. Ö., Baba, C., Yuksel, N., Yildirim, S., Iqbal, S., Sebhaoui, J., Hacımuftuoglu, A., Uhlén, M., Boren, J., Turkez, H., Mardinoglu, A. (2024). Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats. (Manuscript).
[10]
Cadirci, K., Turkez, H., Tozlu, O. O., Yapca, O. E., Bayrak, M., Emsen, B. & Mardinoglu, A. (2024). In Vitro Cytotoxic, Genotoxic, Embryotoxic and Oxidative Damage Potentials by Empagliflozin. Biology Bulletin of the Russian Academy of Science, 51(2), 243-250.
[11]
Abad, N., Buhlak, S., Hajji, M., Saffour, S., Akachar, J., Kesgun, Y. ... Mardinoglu, A. (2024). Unveiling structural features, chemical reactivity, and bioactivity of a newly synthesized purine derivative through crystallography and computational approaches. Journal of Molecular Structure, 1311.
[12]
Hoffmann, U. A., Lichtenberg, E., Rogh, S. N., Bilger, R., Reimann, V., Heyl, F. ... Wilde, A. (2024). The role of the 5' sensing function of ribonuclease E in cyanobacteria. RNA Biology, 21(1), 1-18.
[13]
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).
[14]
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.
[15]
Jotanovic, J., Abdellah, T., Hekmati, N., Sivertsson, Å., Lindskog, C., Uhlén, M. ... Casar-Borota, O. (2024). Transcriptome Analysis Reveals Distinct Patterns Between the Invasive and Noninvasive Pituitary Neuroendocrine Tumors. Journal of the Endocrine Society, 8(5).
[16]
Bidkhori, G. & Shoaie, S. (2024). MIGRENE : The Toolbox for Microbial and Individualized GEMs, Reactobiome and Community Network Modelling. Metabolites, 14(3).
[17]
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).
[18]
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).
[19]
Royer, P., Björnson, E., Adiels, M., Alvez, M. B., Fagerberg, L., Bäckhed, F. ... Bergström, G. (2024). Plasma proteomics for prediction of subclinical coronary artery calcifications in primary prevention. American Heart Journal, 271, 55-67.
[20]
Matić, J., Akladios, F., Battisti, U. M., Håversen, L., Nain-Perez, A., Füchtbauer, A. F. ... Grøtli, M. (2024). Sulfone-based human liver pyruvate kinase inhibitors – Design, synthesis and in vitro bioactivity. European Journal of Medicinal Chemistry, 269.
[21]
Löfgren, L., von Euler Chelpin, M., Bhat, M., Althage, M., Hober, A., Edfors, F. ... Miliotis, T. (2024). Patient-Centric Quantitative Microsampling for Accurate Determination of Urine Albumin to Creatinine Ratio (UACR) in a Clinical Setting. The Journal of Applied Laboratory Medicine, 9(2), 329-341.
[22]
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.
[23]
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).
[24]
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).
[25]
Reitzner, S. M., Emanuelsson, E. B., Arif, M., Kaczkowski, B., Kwon, A. T., Mardinoglu, A. ... Sundberg, C. J. (2024). Molecular profiling of high-level athlete skeletal muscle after acute endurance or resistance exercise : A systems biology approach. Molecular Metabolism, 79.
[26]
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.
[27]
Emanuelsson, E. B., Arif, M., Reitzner, S. M., Perez, S., Lindholm, M. E., Mardinoglu, A. ... Chapman, M. A. (2024). Remodeling of the human skeletal muscle proteome found after long-term endurance training but not after strength training. iScience, 27(1).
[28]
Thalén, N., Moradi, M., Lundqvist, M., Rodhe, J., Andersson, M., Bidkhori, G. ... Rockberg, J. (2024). Tuning of CHO secretional machinery improve activity of secreted therapeutic sulfatase 150-fold. Metabolic engineering, 81, 157-166.
[29]
Akbaba, Y., Kaci, F. N., Arslan, M. E., Goksu, S., Mardinoglu, A. & Turkez, H. (2024). Novel tetrahydronaphthalen-1-yl-phenethyl ureas : synthesis and dual antibacterial-anticancer activities. Journal of enzyme inhibition and medicinal chemistry (Print), 39(1).
[30]
Hudson, E. P. (2024). The Calvin Benson cycle in bacteria : New insights from systems biology. Seminars in Cell and Developmental Biology, 155, 71-83.
[31]
Miao, R., Jahn, M., Shabestary, K., Peltier, G. & Hudson, E. P. (2023). CRISPR interference screens reveal growth–robustness tradeoffs in Synechocystis sp. PCC 6803 across growth conditions. The Plant Cell, 35(11), 3937-3956.
[32]
Woessmann, J., Petrosius, V., Üresin, N., Kotol, D., Aragon-Fernandez, P., Hober, A. ... Schoof, E. M. (2023). Assessing the Role of Trypsin in Quantitative Plasma and Single-Cell Proteomics toward Clinical Application. Analytical Chemistry, 95(36), 13649-13658.
[33]
Uhlén, M. & Lin, F. (2023). Antibody There? : Mapping the Human Proteome with Mathias Uhlén. GEN BIOTECHNOLOGY, 2(3), 167-171.
[34]
Kotol, D., Woessmann, J., Hober, A., Alvez, M. B., Tran Minh, K. H., Pontén, F. ... Edfors, F. (2023). Absolute Quantification of Pan-Cancer Plasma Proteomes Reveals Unique Signature in Multiple Myeloma. Cancers, 15(19).
[35]
Edwards, L. A., Woodhouse, C., Lee, S., Mullish, B. H., Portlock, T., Meoli, L. ... Shawcross, D. L. (2023). Faecal microbiota transplant restores gut barrier function and augments ammonia metabolism in patients with advanced cirrhosis : a randomised single-blind placebo-controlled trial. Journal of Hepatology, 78, S7-S7.
[36]
Möller, M., Jönsson, M., Lundqvist, M., Hedin, B., Larsson, L., Larsson, E. ... Hober, S. (2023). An easy-to-use high-throughput selection system for the discovery of recombinant protein binders from alternative scaffold libraries. Protein Engineering Design & Selection, 36.
[37]
Ovey, I. S., Ozsimsek, A., Velioglu, H. A., Altay, Ö., Mardinoglu, A. & Yulug, B. (2023). EGb 761 reduces Ca2+ influx and apoptosis after pentylenetetrazole treatment in a neuroblastoma cell line. Frontiers in Cellular Neuroscience, 17.
[38]
Kim, W., Li, M., Jin, H., Yang, H., Türkez, H., Uhlén, M. ... Mardinoglu, A. (2023). Characterization of an in vitro steatosis model simulating activated de novo lipogenesis in MAFLD patients. iScience, 26(10).
[39]
Laudette, M., Lindbom, M., Arif, M., Cinato, M., Ruiz, M., Doran, S. ... Borén, J. (2023). Cardiomyocyte-specific PCSK9 deficiency compromises mitochondrial bioenergetics and heart function. Cardiovascular Research, 119(7), 1537-1552.
[40]
Brown, A. A., Hong, M.-G., Dale, M., Uhlén, M., Schwenk, J. M., Viñuela, A. & et al., (2023). Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits. Nature Communications, 14(1).
[41]
Adori, M., Bhat, S., Gramignoli, R., Valladolid-Acebes, I., Bengtsson, T., Uhlén, M. & Adori, C. (2023). Hepatic Innervations and Nonalcoholic Fatty Liver Disease. Seminars in liver disease (Print), 43(2), 149-162.
[42]
Iglesias, M. J., Sanchez-Rivera, L., Ibrahim-Kosta, M., Naudin, C., Munsch, G., Goumidi, L. ... Odeberg, J. (2023). Elevated plasma complement factor H related 5 protein is associated with venous thromboembolism. Nature Communications, 14(1).
[43]
Battisti, U. M., Monjas, L., Akladios, F., Matic, J., Andresen, E., Nagel, C. H. ... Grotli, M. (2023). Exploration of Novel Urolithin C Derivatives as Non-Competitive Inhibitors of Liver Pyruvate Kinase. Pharmaceuticals, 16(5).
[44]
Arslan, M. E., Turkez, H., Sevim, Y., Selvitopi, H., Kadi, A., Oner, S. & Mardinoglu, A. (2023). Costunolide and Parthenolide Ameliorate MPP plus Induced Apoptosis in the Cellular Parkinson's Disease Model. Cells, 12(7).
[45]
Leitao, C. D., Mestre Borras, A., Jonsson, A., Malm, M., Kronqvist, N., Fleetwood, F. ... Lindberg, H. (2023). Display of a naïve affibody library on staphylococci for selection of binders by means of flow cytometry sorting. Biochemical and Biophysical Research Communications - BBRC, 655, 75-81.
[46]
Graves, O. K., Kim, W., Ozcan, M., Ashraf, S., Turkez, H., Yuan, M. ... Li, X. (2023). Discovery of drug targets and therapeutic agents based on drug repositioning to treat lung adenocarcinoma. Biomedicine and Pharmacotherapy, 161.
[47]
Rossi, R., Johansson, C., Heywood, W., Vinette, H., Jensen, G., Tegel, H. ... Ferlini, A. (2023). A Proof of Principle Proteomic Study Detects Dystrophin in Human Plasma : Implications in DMD Diagnosis and Clinical Monitoring. International Journal of Molecular Sciences, 24(6).
[48]
Battisti, U. M., Gao, C., Akladios, F., Kim, W., Yang, H., Bayram, C. ... Grotli, M. (2023). Ellagic Acid and Its Metabolites as Potent and Selective Allosteric Inhibitors of Liver Pyruvate Kinase. Nutrients, 15(3), 577.
[49]
Yulug, B., Altay, Ö., Li, X., Hanoglu, L., Cankaya, S., Lam, S. ... Mardinoglu, A. (2023). Combined metabolic activators improve cognitive functions in Alzheimer's disease patients : a randomised, double-blinded, placebo-controlled phase-II trial. Translational Neurodegeneration, 12(1).
[50]
Turkez, H., Altay, Ö., Yildirim, S., Li, X., Yang, H., Bayram, C. ... Mardinoglu, A. (2023). Combined metabolic activators improve metabolic functions in the animal models of neurodegenerative diseases. Life Sciences, 314, 121325.