Publications
50 latest publications
[1]
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.
[2]
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).
[3]
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.
[4]
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.
[5]
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.
[6]
Geyer, P. E., Hornburg, D., Pernemalm, M., Hauck, S. M., Palaniappan, K. K., Albrecht, V. ... Schwenk, J. M. (2024).
The Circulating Proteome-Technological Developments, Current Challenges, and Future Trends.
Journal of Proteome Research, 23(12), 5279-5295.
[7]
Jimenez-Requena, A., Ajeenah, A., Johansson, C., Naveed, A., Tobin, R., Degan, C. ... Al-Khalili Szigyarto, C. (2024).
Suspension bead array profiling of 1018 serum proteins in search for disease progression biomarkers for Duchenne muscular dystrophy.
Neuromuscular Disorders, 43, 104441.479.
[8]
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.
[9]
Muecke, M., Shoaie, S. & Trebicka, J. (2024).
Terlipressin therapy is associated with increased risk of colonization with multidrug-resistant bacteria in patients with decompensated cirrhosis.
Journal of Hepatology, 80, S203-S203.
[10]
Jin, H., Kim, W., Yuan, M., Li, X., Yang, H., Li, M. ... Mardinoglu, A. (2024).
Identification of SPP1+ macrophages as an immune suppressor in hepatocellular carcinoma using single-cell and bulk transcriptomics.
Frontiers in Immunology, 15.
[11]
Ceyhan, A. B., Kaynar, A., Altay, Ö., Zhang, C., Temel, S. G., Turkez, H. & Mardinoglu, A. (2024).
Identifying Hub Genes and Metabolic Pathways in Collagen VI-Related Dystrophies: A Roadmap to Therapeutic Intervention.
Biomolecules, 14(11).
[12]
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.
[13]
Katsogiannou, A., Karta, D., Di Stefano, A., Oner, S., Arslan, M. E., Mardinoglu, A. ... Cacciatore, I. (2024).
Targeting Alzheimer's disease with novel dual-function 3,5-diaryl-4,5-dihydro-1H-pyrazole-1-carbothioamide derivatives.
European Journal of Medicinal Chemistry Reports, 12.
[14]
Karaman, S., Lehti, S., Zhang, C., Taskinen, M.-R., Kakela, R., Mardinoglu, A. ... Kivela, R. (2024).
Multi-omics characterization of lymphedema-induced adipose tissue resulting from breast cancer-related surgery.
The FASEB Journal, 38(20).
[15]
Meng, L., Jin, H., Yulug, B., Altay, Ö., Li, X., Hanoglu, L. ... Mardinoglu, A. (2024).
Multi-omics analysis reveals the key factors involved in the severity of the Alzheimer's disease.
Alzheimer's Research & Therapy, 16(1).
[16]
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.
[17]
Kotliar, I. B., Bendes, A., Dahl, L., Chen, Y., Saarinen, M., Ceraudo, E. ... Sakmar, T. P. (2024).
Multiplexed mapping of the interactome of GPCRs with receptor activity-modifying proteins.
Science Advances, 10(31), 9959.
[18]
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.
[19]
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).
[20]
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).
[21]
Guner Yilmaz, B., Akgun-Dogan, O., Ozdemir, O., Yuksel, B., Hatirnaz Ng, O., Bilguvar, K. ... Alanay, Y. (2024).
Rapid genome sequencing for critically ill infants : an inaugural pilot study from Turkey.
Frontiers in Pediatrics, 12.
[22]
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.
[23]
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).
[24]
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).
[25]
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.
[26]
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.
[27]
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).
[28]
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.
[29]
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.
[30]
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.
[31]
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.
[32]
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).
[33]
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).
[34]
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.
[35]
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).
[36]
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.
[37]
Bidkhori, G. & Shoaie, S. (2024).
MIGRENE : The Toolbox for Microbial and Individualized GEMs, Reactobiome and Community Network Modelling.
Metabolites, 14(3).
[38]
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).
[39]
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).
[40]
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.
[41]
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.
[42]
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.
[43]
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.
[44]
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).
[45]
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).
[46]
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.
[47]
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.
[48]
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).
[49]
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).
[50]
Hudson, E. P. (2024).
The Calvin Benson cycle in bacteria : New insights from systems biology.
Seminars in Cell and Developmental Biology, 155, 71-83.