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Publications

2025

  1. Akay, S., Nazim, M., Foroughian, R., Kristensen, C. K., Higazy, D., Posselt, D., Ciofu, O., & Yaghmur, A. (2025). Liquid crystalline coatings loaded with colistin for preventing development of biofilms on orthopedic implants. Journal of Colloid and Interface Science, 687, 630–642. https://doi.org/10.1016/j.jcis.2025.02.107
  2. Alturkestani A.A, Jones J.S, Cevik S, Biswas-Fiss E.E, Biswas S.B. Design, Expression, and Purification of a Soluble Form of the Retina-Specific Membrane Transporter, ABCA4, PEDS-24-0036. https://doi.org/10.1101/2025.05.22.655561
  3. Bal K, Küçükertuğrul Çelik S, Şentürk S, Kaplan Ö, Eker EB, Gök MK. Recent progress in chitosan-based nanoparticles for drug delivery: a review on modifications and therapeutic potential. Journal of Drug Targeting. 2025;1–28. doi: https://doi.org/10.1080/1061186X.2025.2502956.
  4. Cevik S, Biswas S.B, Biswas-Fiss E.E. (2025). Assessment of ABCA4 Genetic Variants: Current Landscape and Future Prospects. In: Bowes Rickman, C., Grimm, C., Anderson, R.E., Ash, J.D., Pierce, E., Hollyfield, J.G. (eds) Retinal Degenerative Diseases XX. IWAAL 2011. Advances in Experimental Medicine and Biology, vol 1468. Springer, Cham. https://doi.org/10.1007/978-3-031-76550-6_11
  5. Cevik S, Jones J.S, Biswas S.B, Biswas-Fiss E.E. Deciphering the Impact of ABCA4 Genetic Variants of Unknown Significance in Inherited Retinal Disease Through Computational and Functional Approaches. Advances in Protein Chemistry and Structural Biology (APCSB), Protein Structure Prediction and Analysis (Accepted pre-print)
  6. Demir I, Küçükertuğrul Çelik S, Bal K, Kaplan Ö, Şentürk S, Demir K, Gök MK. Enhancing transfection efficiency of primary cell lines using different terminated PBAE structures without endcapping reaction. Colloid and Polymer Science. 2025. doi: https://doi.org/10.1007/s00396-025-05449-w.
  7. Doğan AHT., Saylam M., Yılmaz S., Parlar S., Ballar-Kırmızıbayrak P., Alptüzün V., 3-(1H-pyrazole-1-yl/1H-1, 2, 4-triazole-1-yl)-N-propananilide Derivatives: Design, Synthesis and Neuroprotectivity Potential Against 6-OHDA Induced Neurotoxicity Model, Turkish Journal of Pharmaceutical Sciences. 2025, 22 (1), 1-9, doi: 10.4274/tjps.galenos.2024.72365
  8. Gökşen Tosun N, Kaplan Ö. Dual targeting of HSP90 and BCL-2 in breast cancer cells using inhibitors BIIB021 and ABT-263. Breast Cancer Research and Treatment. 2025:1–14.
  9. İncir İ, Kaplan Ö. Escherichia coli in the production of biopharmaceuticals. Biotechnology and Applied Biochemistry. 2025;72(2):528–541. doi: https://doi.org/10.1002/bab.2664.
  10. Kaplan Ö, Bal K, Şentürk S, Demir K, Gök MK. Redox-responsive lipoic acid-modified poly (β-amino ester) nanoparticles for enhanced gene delivery. Reactive and Functional Polymers. 2025:106318. doi: https://doi.org/10.1016/j.reactfunctpolym.2025.106318.
  11. Kaplan Ö, Bal K, Şentürk S, Demir K, Gök MK. Silane and amino acid functionalized PBAEs for enhanced gene delivery: Synthesis, characterization, and transfection efficiency. Journal of Drug Delivery Science and Technology. 2025;109:106990. doi: https://doi.org/10.1016/j.jddst.2025.106990.
  12. Şentürk S, Kaplan Ö, Bal K, Baş Topcu KS, Gök MK. Thiolated layered double hydroxide-based nanoparticles: A study on mucoadhesiveness and cytotoxicity. Colloids and Surfaces A: Physicochemical and Engineering Aspects. 2025;704:135461. doi: https://doi.org/10.1016/j.colsurfa.2024.135461.
  13. Tantan Y, Kaplan Ö, Bal K, Şentürk S, Eker Fidan EB, Çelik S, et al. Tricine-modified chitosan as a strategy for enhancing hydrophilicity and gene delivery. Carbohydrate Research. 2025;547:109326. doi: https://doi.org/10.1016/j.carres.2024.109326.

2024

  1. Akar, Z., Akay, S., Ejder, N., & Özad Düzgün, A. (2024). Determination of the Cytotoxicity and Antibiofilm Potential Effect of Equisetum arvense Silver Nanoparticles. Applied Biochemistry and Biotechnology, 196(2), 909–922. https://doi.org/10.1007/S12010-023-04587-7
  2. Akay, Ş and Özdilek, H., “Kitosan parçacıklarının üretimi için düşük maliyetli mikrosistemlerin tasarımı ve fabrikasyonu,” Gazi Üniversitesi Mühendislik Mimarlık Fakültesi Dergisi, vol. 39, no. 4, pp. 2363–2372, May 2024, https://doi.org/10.17341/gazimmfd.1299367
  3. Akay, S., & Yaghmur, A. (2024). Recent Advances in Antibacterial Coatings to Combat Orthopedic Implant-Associated Infections. Molecules 2024, Vol. 29, Page 1172, 29(5), 1172. https://doi.org/10.3390/molecules29051172
  4. Akay, S., Yüksel, G., & Özad Düzgün, A. (2024). Investigation of Antibiofilm and Antibacterial Properties of Green Synthesized Silver Nanoparticles from Aqueous Extract of Rumex sp. Applied Biochemistry and Biotechnology, 196(2), 1089–1103. https://doi.org/10.1007/s12010-023-04592-w
  5. Cevik S, Biswas SB, Ghosh A, Biswas-Fiss EE. Virus-like particles as robust tools for functional assessment: Deciphering the pathogenicity of ABCA4 genetic variants of uncertain significance. J Biol Chem. 2024 Oct;300(10):107739. doi: 10.1016/j.jbc.2024.107739. Epub 2024 Aug 31. PMID: 39222682; PMCID: PMC11474199.
  6. Eker Fidan EB, Bal K, Şentürk S, Kaplan Ö, Demir K, Gök MK. Enhancing gene delivery efficiency with amphiphilic chitosan modified by myristic acid and tertiary amino groups. International Journal of Biological Macromolecules. 2024;282:136775. doi: https://doi.org/10.1016/j.ijbiomac.2024.136775.
  7. Gökşen Tosun N, Kaplan Ö, Özgür A. Evaluation of Anticancer and Antimicrobial Potentials of Tarantula cubensis Venom (Theranekron® D6). Erzincan University Journal of Science & Technology. 2024;17(3).
  8. Güzel Ö, Kehoe P.G. (2024). The Contribution of the Renin-Angiotensin System to Alzheimer’s Disease. In: Kidd, E.J., Newhouse, P.A. (eds) Neurobiology of Alzheimer's Disease. Current Topics in Behavioral Neurosciences, vol 69. Springer, Cham. https://doi.org/10.1007/7854_2024_525
  9. İncir İ, Kaplan Ö. Escherichia coli as a versatile cell factory: Advances and challenges in recombinant protein production. Protein Expression and Purification. 2024;219:106463. doi: https://doi.org/10.1016/j.pep.2024.106463.
  10. Kaplan Ö, Gök MK, Pekmez M, Erden Tayhan S, Özgümüş S, Gökçe İ, et al. Development of recombinant protein-based nanoparticle systems for inducing tumor cell apoptosis: In vitro evaluation of their cytotoxic and apoptotic effects on cancer cells. Journal of Drug Delivery Science and Technology. 2024;95:105565. doi: https://doi.org/10.1016/j.jddst.2024.105565.
  11. Kaplan Ö, Gökşen Tosun N. Molecular pathway of anticancer effect of next-generation HSP90 inhibitors XL-888 and Debio0932 in neuroblastoma cell line. Medical Oncology. 2024;41(8):194. doi: 10.1007/s12032-024-02428-z.
  12. Kaplan Ö. Evaluation of combined use of hsp90 inhibitor mpc-3100 and traditional cancer drug 5-fu on liver cancer cell lines. Journal of Scientific Reports-A. 2024(055):60–69.
  13. Tayler HM, MacLachlan R, Güzel Ö, Fisher RA, Skrobot OA, Abulfadl MA, Kehoe PG, Miners JS. Altered Gene Expression Within the Renin-Angiotensin System in Normal Aging and Dementia. J Gerontol A Biol Sci Med Sci. 2024;1:79(1):glad241.
  14. Yılmaz S., Bedir E., Ballar-Kırmızıbayrak P., Multi-Targeted Effects of Novel Cycloastragenol Derivatives: Enhancing NRF2, Proteostasis, and Telomerase Pathways with p53 Modulation to Delay Replicative Senescence, Biorvix, 2024, doi: https://doi.org/10.1101/2024.08.12.607434

2023

  1. Akay, Ş., & Eda Kuş, S. (2023). Metallic Nanoparticles: Synthesis and Applications in Medicine. 57–80. https://doi.org/10.2174/9789815179422123080006
  2. Akay, Ş., & Sefaoğlu, M. (2021). Production and characterization of zinc oxide nanoparticles in microsystems via green synthesis. Gümüşhane University Journal of Science and Technology, 11(2), 315–324. https://doi.org/10.17714/gumusfenbil.819717
  3. Alkan C, Gökşen Tosun N, Kaplan Ö. Synthesis and characterization of dicarboxylic acid esters of 1-hexadecanol for a thermal energy storage application range of 50–55°C. Energy Technology. 2023;11(8):2300104.
  4. Aykur M, Gökşen Tosun N, Kaplan Ö, Özgür A. Efficacy of the greenly synthesized silver, copper, and nickel nanoparticles using Allium tuncelianum extract against Acanthamoeba castellanii. Journal of Drug Delivery Science and Technology. 2023;89:105013. doi: https://doi.org/10.1016/j.jddst.2023.105013.
  5. Bal K, Şentürk S, Kaplan Ö, Gök MK, Pabuccuoğlu SK. Optimization studies of Mg/Al-NO₃ layered double hydroxide nanoparticles by hydrothermal treatment. ALKÜ Fen Bilimleri Dergisi. 2023;5(3):163–175.
  6. Cevik S, Biswas S.B, Biswas-Fiss E.E. Structural and Pathogenic Impacts of ABCA4 Variants in Retinal Degenerations-An In-Silico Study. Int J Mol Sci. 2023 Apr 14;24(8):7280. doi: 10.3390/ijms24087280. PMID: 37108442; PMCID: PMC10138569.
  7. Cevik S, Wangtiraumnuay Schelvergem K.V, Tsukikawa M, Capasso J, Subhasis B. Biswas, Bodt B, Levin A.V, Biswas-Fiss E. Protein modeling and in silico analysis to assess pathogenicity of ABCA4 variants in patients with inherited retinal disease. Mol Vis. 2023 Oct 25;29:217-233. PMID: 38222458; PMCID: PMC10784225.
  8. Kaplan Ö, Nazan GT, İsa G, Alkan C. Diacid esters of 1-dodecanol as new alternatives to solid-liquid phase change materials for solar heat storage systems. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects. 2023;45(1):608–622. doi: 10.1080/15567036.2023.2172103.
  9. Kaplan Ö, Tosun NG. Biosynthesis of iron, copper and silver nanoparticles using Polygonum cognatum and Tragopogon porrifolius extracts and evaluation of their antimicrobial potentials. Düzce Üniversitesi Bilim ve Teknoloji Dergisi. 2023;11(4):2155–2167.
  10. Kaplan Ö, Truszkowska M, Kali G, Knoll P, Blanco Massani M, Braun DE, et al. Thiolated α-cyclodextrin: The likely smallest drug carrier providing enhanced cellular uptake and endosomal escape. Carbohydrate Polymers. 2023;316:121070. doi: https://doi.org/10.1016/j.carbpol.2023.121070.
  11. Kaplan Ö. Synergistic induction of apoptosis in liver cancer cells: exploring the combined potential of doxorubicin and XL-888. Medical Oncology. 2023;40(11):318. doi: 10.1007/s12032-023-02181-9.
  12. Korkmaz N, Kısa D, Kaplan Ö, Tosun NG, Özgür A, Imamoğlu R, et al. A silver compound with potential applications as an anticancer, antibacterial, antifungal, and anti-Alzheimer’s agent. Chemistry & Biodiversity. 2023;20(6):e202300038.
  13. Küçüksolak M, Yılmaz S, Ballar-Kırmızıbayrak P & Bedir E, Potent telomerase activators from a novel sapogenin via biotransformation utilizing Camarosporium laburnicola, an endophytic fungus, Microbial Cell Factories volume, 2023, 22, Article number: 66, doi: https://doi.org/10.1186/s12934-023-02069-3
  14. Soylu SF, Zıdan A, Tosun NG, Kaplan Ö, Gökçe İ. Optimizing the synthesis of folic acid conjugated silver nanoparticles by Box-Behnken design to target breast cancer cells. ALKÜ Fen Bilimleri Dergisi. 2023;5(3):100–117.
  15. Tatar İ, Uysal Ş, Yılmaz S, Tarikogullari A, Ballar-Kirmizibayrak P, Soyer Z, Design, synthesis, and biological evaluation of some novel naphthoquinone-glycine/β-alanine anilide derivatives as noncovalent proteasome inhibitors, Chemical Biology&Drug Desing, 2023, 101 (6), 1283-1298, https://doi.org/10.1111/cbdd.14212
  16. Tayler HM, MacLachlan R, Güzel Ö, Miners JS, Love S. Elevated late-life blood pressure may maintain brain oxygenation and slow amyloid-beta accumulation at the expense of cerebral vascular damage. Brain Commun. 2023;5(2):fcad112.

 2022

  1. İlhan, R., Üner G., Yılmaz S., Sahar-Atalay E., Çaylı S., Erzurumlu Y., Gözen O., & Kirmizibayrak-Ballar P, Novel regulation mechanism of adrenal cortisol and DHEA biosynthesis via the endogen ERAD inhibitor small VCP-interacting protein, Scientific Reports, 2022, 20452322, 12, https://doi.org/10.1038/s41598-022-04821-y
  2. Yılmaz S., Bedir E. & Kirmizibayrak-Ballar P., The role of cycloastragenol at the intersection of NRF2/ARE, telomerase, and proteasome activity, Free Radical Biology and Medicine, 2022, 0891- 5849, 188, https://doi.org/10.1016/j.freeradbiomed.2022.06.230
  3. Yılmaz S., Tok F., Sahar-Atalay E, Kaymakcıoglu B. & P Kirmizibayrak-Ballar P., Induction of Divergent Cell Death Pathways by Urea and Carbohydrazide Derivatives, Anti-Cancer Agents in Medicinal Chemistry, 2022, 1871-5206, 21, https://doi.org/10.2174/1871520621666210528153949

2021

  1. Duman S., Ekiz G., Yılmaz S., Yusufoglu H., Kirmizibayrak-Ballar P & Bedir E, Telomerase activators from 20(27)-octanor-cycloastragenol via biotransformation by the fungal endophytes, Bioorganic Chemistry, 2021, 0045- 2068, 109, https://doi.org/10.1016/j.bioorg.2021.104708
  2. Güzel Ö, Duman S, Yılmaz S, Karakoyun Ç, Kul D, Pirhan AF, Bedir E. Screening of cytotoxicity and DNA topoisomerase IIa inhibitory activity of Turkish Onosma species. Turkish Journal of Botany. 2021;45(8):6.
  3. Güzel Ö., Duman S., Yılmaz S., Karakoyun Ç., Kul D., Pirhan A.F. & Bedir E., Screening of cytotoxicity and DNA topoisomerase IIa inhibitory activity of Turkish Onosma species, TURKISH JOURNAL OF BOTANY, 2021, 1300-008X, 45, https://doi.org/10.3906/bot-2108-23
  4. Kırtel O., Aydın H., Toksoy Öner E, Fructanogenic traits in halotolerant Bacillus licheniformis OK12 and their predicted functional significance, Journal of Applied Microbiology, 2021, 131 (3), 1391-1404 https://doi.org/10.1111/jam.15015. https://doi.org/10.1111/jam.15015"
  5. Saylam M., Doğan Tarıkoğulları A.H., Yılmaz S. & Kirmizibayrak-Ballar P., Neuroprotective activity studies of some phenylacetamide derivatives bearing 1H-pyrazole or 1H-1,2,4-triazole, Bioorganic and Medicinal Chemistry Reports, 2021, 2667-6028, http://doi.org/10.25135/acg.bmcr.26.2111.2255.
  6. Tayler H, Miners JS, Güzel Ö, MacLachlan R, Love S. Mediators of cerebral hypoperfusion and blood-brain barrier leakiness in Alzheimer’sdisease, vascular dementia and mixed dementia. Brain Pathol. 2021;31(4):e12935.
  7. Tok F., Kaymakcıoglu B., İlhan R., Yılmaz S., Kirmizibayrak-Ballar P & Taşkın-Tok T., TOK, Design, synthesis, biological evaluation and molecular docking of novemolecules toto PARP-1 enzyme, TURKISH JOURNAL OF CHEMISTRY, 2019, 1300-0527, 43, 5, 1290-1305
  8. Uysal Ş., Soyer Z, Saylam M., Doğan Tarıkoğulları A.H., Yılmaz S., & Kirmizibayrak-Ballar P., Design, synthesis and biological evaluation of novel naphthoquinone-4- aminobenzensulfonamide/carboxamide derivatives as proteasome inhibitors, European Journal of Medicinal Chemistry, 2021, 0223- 5234, https://doi.org/10.1016/j.ejmech.2020.112890.
  9. Yılmaz S., Alkan T., & Kirmizibayrak-Ballar P., A new underlying mechanism for the neuroprotective effect of bosutinib: Reverting toxicity induced PARylation in SIN1-mediated neurotoxicity, Journal of Biochemical and Molecular Toxicology, 2021, 1095- 6670","1099-0461, https://doi.org/10.1002/jbt.22915